Eh, matter of interpretation. Orks don't have souls, squigs don't have souls, so what does it really matter, really?
That being said, it'd likely still be a better option, if only because squigs are considered animals rather than sentient beings...
*eats some green with the blessing of the Emperor*
Given the Orcish habit of eating humans, we can probably assume Orchish biochemistry isn't inherently toxic to humans. Probably...
But Orcs are full of fungi and algae that can fairly intelligently repair Orch physiology, which happens to be remarkably similar to the human, at least in broad strokes. So assuming any ingested bits of Orc isn't entirely digested, or that human digestion simply isn't fast enough, it does strike me as suitably 40K scienc'y that it would all bloom to life within the poor human host and rapidly murder the hell out of him in a grotesque & mushroom garden-like fashion.
As for food taboos, they generally have to do with the edibility of the material, and soul isn't a very common criteria. In fact, it's occasionally the justification for eating things people otherwise wouldn't eat in a million years - like the pulverised skulls of family members, for example.
If Orcs are in fact edible, I can easily imagine that Orc-plagued feral worlds will have Orc-eating traditions. Perhaps tribal warriors would eat the brains or biceps of a particularly cunning or large Orc before battle, to absorb its strength, or something along those lines. We Earthlings have done such things, though we've substituted Orc with Human, since the former is kind of scarce around here.
Orks have a TB of 8 in Dark Heresy. How can he punch them to death? The must damage he can do with his fists is 1d5+3, if he has Crushing Blow.