What if souls aren't really souls, and they're just a representation of the energy left inside a corpse?

All in-game healing (At least by supports. Medpacks might be different.) is apparently done by nanites. Maybe Reaper's nanites just highlight potential energy sources, and when they're close enough to a corpse of someone has recently been killed they can collect any remaining energy so they can heal him. Since Reaper wouldn't know about the nanites, it's just assumed that what he's absorbing is a soul.

Mercy still sees "souls" but doesn't absorb them, but it could still be a similar thing. Her suit or her nanites look out for recent corpses, and when she uses her ultimate the energy she's stored is used to revive those team mates.

Maybe the difference between Reaper and Mercy's nanites is that Reaper's nanites: 1) Work at an accelerated rate (As we knew before), and 2) don't have the same fail-safes as to what kinds of energy they can use to recharge and, while they can't take energy directly from people, can still take energy from corpses. (Which is probably something Mercy would have disapproved of since those people don't have to die.)

Basically Reaper's nanites are a buggy, broken mess since their development was rushed and made to release at a tight deadline, while Mercy's are bug free since she had time to continue development at her own pace and focus on putting in fails-safes and calibrating settings. :P

I don't think souls really make too much sense in a game that tries to explain everything else with science and future technology rather than magic and spirituality.