Is there any cannon rule that would prevent a disgruntled group of ex-cybermancy researchers from kidnapping homeless people, loading them up with cheap cyberware untill they die of essence loss, then summoning Ally Spirits to inhabit their not-quite-metahuman anymore corpses?
It seems like a cost effective way to create a loyal army of cybernetic tanks, but I don't have MitS so i'm not sure what the limitations of Inhabitation are.

I don't think this would work under the canon limits of inhabitation. (I.e. only in nonawakened animals or specially prepared foci.) Also, though there's no ruling on this one way or another as far as I know, I wouldn't have nonpassive cyberware (anything but bone lacing, dermal plating, etc) continue to work after the host is dead.

Yeah, anything relying on the nerve system would at best be subject to the same effects a ghoul's cyberware experiences during tranformation.

Technically I wouldn't say anything stands in the way of summoning ally spirits into corpses, though it isn't strictly canon for ally spirits.

You're just describing canon zombies. Structural cyber works just fine for them. You don't even need a group of disgruntled ex-cybermancy mages; a perfectly ordinary Petro Voudounista could do the trick.

You could also construct a drone to use as a homunculus and have the ally inhabit it. I think (I may be wrong, haven't ever tried it) most thing that can be put into a cybernetic limb can be put into a mechanical arm.

The ally would get some armor bonuses, the force of the foci could increase its physical stats and it relies on the magician for mental stats.