HOLY SHIT do you know what I realised earlier when watching this episode?
Roy doesn’t know what happened in the phone booth when Hughes was killed. He doesn’t know that Envy transformed into Maria Ross before transforming into Gracia, and he doesn’t know that Hughes was aware it was a shapeshifting homunculus pointing a gun at him. All he knows is what Envy says here - that Envy definitely pulled the trigger whilst in the form of Gracia.
So it’s possible that Roy thinks Envy took the form of Gracia and shot Hughes without revealing that he was a shapeshifter. And if that were the case, it would mean that Hughes would have seriously believed it was his own wife shooting and killing him.
No wonder Roy got so pissed.