Spoiler discussion inside since the TV recap ignored the last few seconds of the episode entirely.
The TV Recap on the front page dedicated 1 sentence to the last 15 seconds. Here's the deal. It wasn't a dream. There's no way. And here's why. His dream quoted Sara's line exactly. "What are you doing here." If Roy wasn't really there I don't think that line is inserted into the nightmare.
I figure 3 possible reasons Roy killed Sara.
1) It really did look like Mirakuru induced rage. I realize he's been cured, but he threw those arrows he didn't shoot them...
2) Brainwashed by Waller. That would help explain the nightmares as his subconscious is remembering what happened.
3) Blackmailed by Waller. Oliver was blackmailed. Perhaps Roy is being blackmailed as well.