Yeah... but if the issue is them firing on the thing with ship weapons, then securing the docking clamp doesn't actually win us much, from what I can see.
also, I still think that limiting our drone losses is pretty important. We need those drones. If fighting continues we'll need them immediately, and if it doesn't, we'll want to have them around for the continued repairs and such.
To elaborate some my thought process was sorta along the lines of like- "if we have control over the smuggler vessel, we're probably in a better place to preserve it" y'know? Since I figure a smallish private ship in the Imperium probably has at least a few tools and tricks to avoiding getting pasted by Imperial Navy vessels or the like. Whether that's like- firing off Wild Weasel-esque decoys, some kind of jamming, or just being able to punch it- possibly while towing a larger vessel.
I don't think the smuggler's ship is doomed if we don't take this option right now, to be clear. Just that it's left vulnerable for a little while longer which might have Consequences depending on what goals or objectives the Inquisitorial forces are able to accomplish and what the Mechanicus contingent decides to do.
Tbc though, I'm pretty much fine with two of the three priorities we've settled on. I think protecting the Gene Creche and activating the War Deck, waking up the batroids and all their buddies, are both solid calls. In addition to just, like, liking the Smugglers, their interactions with Nemesis, and protecting them being morally the Right Thing To Do, the Gene Creche is irreplaceably valuable and probably the last remnants of any number of species the Imperium has exterminated. And the War Deck gives us more immediate options and resources after we decapitate (possibly literally) the Inquisition's leadership here.
Honestly, icing Khan isn't even a bad call either. In addition to being the last member of the Inquisitorial staff with any training or shreds of command to him, he's a genuinely dangerous opponent in a personal capacity and is poised for a bloody, possibly suicidal vendetta so, y'know, good to just nip that shit in the bud before it spirals.
It's going to be interesting, imo, because I'm pretty sure with the Cadians in tatters and the Inquisitor and his retinue getting Avatar'ed, Magos
Skyre is the ranking authority. And what he decides to do is, very probably, not what the Ordo Xenos would have preferred. Although not sure if that means anything good for us.