No man it'll be fine as long as it's not really squished. I say if you can fit a finger down there you aren't restricting the exhaust at all. Remember that you have a round pipe connected to a rectangular exhaust port so the end of the pipe is probably doing most of the restriction by itself. If you did really squish the sucker just put it in the vise again the opposite way and heat it with a torch then gently clamp the pipe down until its more uniform. This may square it off a bit but then just repeat by doing quarter turns, heat and squish but either way it should get the flow correct again. If you have divots in the metal those can be easily ground out with a dremmel or bench grinder. Just don't grind it down far enough to weaken the metal or create holes and it should be as good as new. For future reference though its better to screw the manifold into a block of wood rather than placing the thing directly in a vice.
