I don't mind the line you took at all, this is a 5/1 SNG and its not that unlikely he limped with suited trash. You have around a 20% chance to hit the flush on the river and its only queen high. With that considered I think you made a good lay-down.

The flop raise shows strength and he re-raises, I think the call is ok as a fold might make people take shots at you on the flop later, when the turn card doesn't bring a and he goes all in its an easy fold.