Damaged rim or just the tube valve?
It's possible you damaged your rim, but it should be very easy to check. Turn the bike over and spin the wheel and eyeball it both side to side and up and down. If you have put a flat spot in the rim it should be very noticeable.

It's more likely that it is just the way the (flat) tyre is sitting on the rim, which might well be affected by the valve. If you've got a narrow tyre and a lockring on the valve, that may be holding the tyre on the rim at that point only, causing a wobble when that part of the wheels hits the ground.