Previously, it was suggested that critical thought must be given to the existing doctrines of the Adeptus Mechanicus in order to determine what purpose they are intended to serve and whether or not that purpose is still valid after the birth of the Abomination. No area of doctrine or dogma must be immune to this line of inquiry. This includes the matter of xenotechnology. Current dogma holds that xenotechnology is a perversion of the true path.
Currently that dogma is allowed to go unquestioned, but it is known that mindless, unquestioning xenophobia is one of the paths to the Abomination. As such, the entire notion must be analyzed through the lens of critical thought. The questions must be asked.
Firstly, why does the doctrine exist? It is known that during the Great Crusade, many xeno species were encountered and fought, and revelations by Saint Lin tell us that many were corrupted by the influence Chaos. The adherents of Chaos corrupt everything they touch, and that includes their technology. Given the Emperor was intent on hiding the existence of Chaos from humanity at the time, it was logical that he wouldn't want the Adeptus Mechanicus studying potentially Chaos corrupted as the taint would spread to them. A near complete ban on xenotechnology study was sensible given the Emperor's goals at the time, so that likely answers the question as to the doctrine's original intended function.
However, now that humanity knows of Chaos, the risks it represents, and how to look for signs of its taint the doctrine needs to be reevaluated. Is xenotechnology intrinsically a perversion of the true path, or is it simply the risk of Chaos that is the problem? The answer is not simple, but can likely be found by a cursory examination of a few different xeno species and their technology.
Dark Eldar - These vile creatures have vast amounts of knowledge, and many of their machines are dedicated towards causing pain and suffering. Even after being freed from the grasp of Slaanesh, we have seen that many of these monsters continue to revel in sadism for no greater purpose. And what good does it doe them? While they could not be explicitly corrupted before, now they no doubt will be. We have already seen that the Dark Eldar on Fjol IV were experimenting with daemons.
Necrons - The Necrons have no reason to fear Chaos corruption, but that does not make their technology pure. They are soulless things, their mechanisms being without true Machine Spirits. Humanity is defined by the human soul, and cannot go down the path that the Necrons were taken by the C'tan. Further, many Necrons are dedicated towards the destruction of life and harvest of more souls for the C'tan, things that are against the interests of humanity.
Orks - The Orks seem to possess technology, but it is false. It is not created by true knowledge, nor does it operate on it beyond the most base level. A human attempting to wield Ork technology will find it unlikely to work at best and explosively dangerous at worst, even as it might work for an Ork. Ork technology represents a false path. Further, the Orks by their very nature seek nothing but violence and war, not for the sake of protecting something greater, but for its own sake.
Based on these examples, it might be said there are at least three aspects of purity that they fail to meet.
Purity of Spirit - Technology of the true path both possesses a Machine Spirit and is free of the influence of Chaos.
Purity of Purpose - Technology of the true path is useful for noble purposes.
Purity of Knowledge - Technology of the true path is based on real knowledge that humans can comprehend.
There may be more aspects of purity to consider, but these three seem a good start for any assessment of technology of any origin, be it xeno or human. The monstrosities created by the Dark Mechanicus certainly fail to meet all three of these measures on a regular basis, after all, even if those wretches might not be defined as human anymore.
So then, are there any xeno species whose technology isn't corrupt? It's quite possible. One race to look at is the Quartok.
Purity of Spirit? The Quartok do have souls, so their machines may possess Machine Spirits even if they do not make proper observances towards them. They are aware of Chaos and abhor it properly, and none of their technology has thus far shown any influence of Chaos.
Purity of Purpose? They use their technology much as humans do, if to the good of their own kind rather than to that of humanity. Though their military technology was used against humanity in the past, they honestly believe this to have been in self defense against human aggression, and no rational species would not defend itself from attack.
Purity of Knowledge? Their technology is inferior to ours in most areas, and only somewhat more so in areas of automation, though the humans of the Dark Age of Technology likely surpassed even that. As such, it can likely be comprehended, and that can be verified when the deal for their protectorate goes through and they hand over their full technological and scientific knowledge.
A cursory examination seems to indicate their technology is not far deviated from the true path, and could be reformed to be correct as needed. Of course, that is a cursory glance only and proper caution should be taken if the technology is ever studied.
So, it's likely a good idea to have the Adeptus Mechanicus study xenotechnology to see what can be gained, so long as it is done cautiously. However, it will take some time to gain acceptance of this notion among the greater AdMech. Continued pursuit of critical thinking and changes to rhetoric are a major part of that.
One practical way to begin implementing study of xenotech sooner is advocating that learning how to turn dangerous xenotech off safely is necessary - the explosion of the Dark Eldar reactor at Fjol IV shows that ignorance of xenotech can have a deadly cost, so sufficient understanding to disable it without causing catastrophic loss of life is likely a politically acceptable argument. The first step to achieving that would likely be to have some members of the Mechanicus go through the new xeno language courses being offered in the Collegia, so they do not have to work through a translator who may not be able to fully convey what something means in a short time during a crisis. Once that level of study is well accepted, pushing for further study should become possible.
Avoiding Unnecessary Unrest From This Subject Matter
First, it should be noted that the above is a long term strategy. Ideas should be introduced with proper timing, and be as gradual as needed, to avoid doing more harm than good. Given the degree of Dark Age technology being gained, research of xenotechnology is not the highest priority for reforms, even if it needs to be done in the long term.
For introducing the critical thought portion, it may be best not to mention the Quartok as a positive example, at least initially. Focusing on the negative examples of xenotechnology and giving a "why" to their impurity without actually contradicting the existing doctrine, but at the same time not closing off all xenotechnology as immediately impure. With time members of the Mechanicus may come to the correct conclusions on their own, making it easier to endorse study of specific "safe" xenotechnology later on.
In regards to the "safe shutdown" project, it may be a good idea to carefully select a few well known and respected members of the conservative factions to be included as part of it. They can be touted as necessary for the project due to being "voices of necessary caution" and "having proven records for standing against corruption". Politically, this will make the project harder to criticize, as the conservatives are included in the project and makes it so they know their voices are being heard by the Fabricator General. While this might slow down the study of xenotech in the short term, in the long run it could make for a smoother transition.
Further, it can be stated truthfully that the Mechanicus has had trusted Magos studying xenotechnology with great caution, and that establishing the project is merely a part of slow re-establishing expertise that has been cut off. A specific example of this to use can be the sale of the wrecked Necron cruiser that Atlas purchased from Avernus for study - given many of the tech-priests in the Imperial Trust are from Atlas, it should show that even their old leadership accepted some degree of study of xenotechnology.