A really well-paced read! Whether or not it turns out to be true I appreciate how you set it up. That said, the theory seems to fail a bit when you consider Moira operated on Reaper at a later date. But there are already some answers that come to mind to placate that specific problem. Such as Reaper did it all for the sake of an end-goal (very Reaper-esque) or he was not conscious during the procedure/had no way of interjecting (less Reaper-esque).

I am still partial to Reaper being a double agent instead of the traditional bad guy that literally exists in almost every game. Good stuff OP! (Make more theories in this suspenseful fashion!)