I think that we’ve got to think about the reality of the situation. The stone was there, already made, and it wasn’t just going to go away. Those souls were still there, basically trapped in (I assume) eternal torment until they’re used. So the grim reality of the stone is that it’s made to be used, all of those people are already dead and the stone is only prolonging their suffering (therefore making using it rather like a mercy killing), and Roy was already going to help restore Ishval and attempt to reverse the Ishvalan policy and end the racism. And unfortunately, that absolutely 100% required the use of his eyesight (as the military definitely would have given him an honorable discharge had he stayed blind).
Add all of this to the fact he had absolutely zero control or agency over the loss of his eyesight (being forced into human transmutation) and pushed for Havoc to be healed before him, and I see Roy accepting the Philosopher’s Stone as a ‘it’s the best way’ situation as well as a mercy killing for the Ishvalans trapped within the stone. No, he had no right to use it, but the other question that arises is “Well, who did?” No one except the Ishvalans, really, and we all know that like 99.9% of them would have flat-out refused (given that a) they hate alchemy and b) it’s the souls of their dead brethren like why would they use it). Roy definitely knows he has no right to use it, and Marcoh does too. However, Maroh using it to heal Roy and Havoc, two people that are definitely 100% going to use their newly healed bodies to lead the restoration of Ishval and who have the power and means to do so is definitely the best outcome in this horrible situation.
Plus, Roy never had the 100% strong moral code against killing/using philosopher’s stones that Ed did. And that’s okay, that he sees the world in shades of grey. That’s just how I see it, personally.
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