The puffer should be able to expel most of the air on its own, if he is eating fine and doesn't seem affected, I would not be too overly concerned (bouyancy problems, etc.). You could move him to QT, just to keep a good eye on him, however it is a very remote chance that they would actually kill other tank inhabitants unless they actually devoured the dead fish. Puffers store the toxin (Tetrodotoxin) in their tissues, liver, and gonads. It is more of a defensive toxin (as in if you eat me, I am taking you down too!) than it is offensive, as say the blue ringed octopus that uses the same toxin in its venom.
I will run this by the resident puffer expert at my site just to make sure though.
I do have an excellent article on my site: Puffer Care and Information
which includes the following on how to remove air from a puffer that is unable to do so on its own..........
"Those puffers that can't release the air can actually become stressed enough that they perish. If your puffer does become inflated with air, there is a method of helping it release it. Which needs steady but gentle hands. You will have to hold you puffer with your hands, with it's head facing up, then begin to gently massage the belly of the fish upwards to it's chin. This will help the valves release and the air to escape from the upward facing puffer's mouth."
I hope this helps!