If I am going to eat somebody, it might as well be you.
This is acceptable. The prohibition against futurive will is a prohibition against that word in that sense, not the future reference. In any case, be going to in this context is present-focused: it expresses present intention or expectation of a future event.
It might as well be you literally means “You would serve as well as (or better than) another as object of my eating.” In actual use, however, there is no modality or tentativeness here. Might as well in this context announces a decision to accept an invitation or opportunity:
A: Wanna go grab a beer?
B: Might as well.
(Actually, in my dialect it would be “Mought's well. Can’t dance, and it’s too wet to plow.”)
The sentence may be paraphrased “Given my intention of eating somebody, I have decided to eat you.”
If I was going to eat somebody, it ... ?
This is trickier. Was here is acceptable colloquially as a variant of formal were. In some contexts it might express uncertainty or hypotheticality, but in the context of my intention it almost has to express counterfactuality: “I do not at present intend to eat somebody, but if I did ... ”
Consequently, it might as well be you cannot follow this. Grammatically it would be acceptable, but semantically the firm intention it expresses does not suit a counterfactual situation. And since its past-irrealis form (might) is already completely ‘modalized’, it cannot be modalized any further. To the best of my knowledge, even dialects which accept modal stacking will not permit this:
∗ ... it would might as well be you.
So you have to find an alternative expression. The closest I can get to a counterfactual version of the original is something like this:
If I was gonna eat somebody it’d definitely be you.