The thing is the Webway also depends on the Warp at the most basic level, it runs though the warp, which means that on order to do any kind of repairs or heck to add new sections to it you need warp-smiths of some kind. There is a
reason the Eldar have Bonesingers and it's not for fashion. That is what they make their stuff out of, including but not limited to what repairs they can still make to the Webway. So unless the Emperor can make the whole thing himself or only with the aid of Magnus it makes on sense for him to do the isolation first and then train psykers to not be Chaos bait. He should have started in the opposite order... and for that purpose the navigators would have been a potential resource. Here we have a sort of psyker who is highly resistant to the Warp (if they are even a psyker as
@Alratan said there is a case to be made that they act on the warp without touching it). So why isn't he recruiting them, why isn't he recruiting anyone to make this super secret Webway project? I think the Emperor does not
have all the pieces himself to get from humanity isolated from the Warp to all of them rejecting Chaos.
As for the reason why he might have to kill the Navigators though, I agree that it would not be any kind of dislike of them as abhumans, I do not think he even
dislikes Abhumans really, but that does not really matter against the reality of the power and prestige he would be taking from them with his magnum opus, casting them to the tender mercies of their baseline human kin This finally is where we are at the moment, stuck between the implacability of the Golden Man who does not value the Navigators as more than a stopgap and the Navigators themselves who do not want to get killed, with or without the complicity of Imperial law.
I think what we need to do is... show him that it does not work, his half designed plan, we have Lorgar's memories of betraying the Ultramarines, Chaos Primarch Lorgar. It is
risky at hell to show him that, but I think it is the one thing that can convince him that he does not know best and that he might have to redesign his plans. Otherwise weare trimming around the edges of a plan we do not understand and which we know is doomed to fail in canon, not so much because of circumstance as because the Emperor does not get the very humans he si trying to save. Heck I am not even sure he understands the Prmarchs and he
made those.