Had the time to act not come soon, John would have been in danger of possibly blowing the plan, watching Jo and then Dean thrown around. Words, words could be fixed later, but he wasn't taking either of them back in pieces. He refused.
The minute Azazel was in the trap, John was out of his hiding spot and advancing on them, strides eating up the ground as he raised the gun and fired. However, it wasn't the Colt fire, just a regular gun in his other hand – nothing short of the armies of Hell would be getting the Colt out of his hand now. Sure, a regular shot wouldn't do a hell of a lot in damage, but all John needed it to do was but that demon further off balance and let go of Dean.
Then he was going to look that thing in the eyes, the creature that had destroyed his life and continued to affect it, one last time before he destroyed it once and for all, by his own hand this time, instead of crawling out of Hell and being the aide needed for someone else to do it.