All that needs to happen is for his signature to have something ridiculous like a 60s cooldown instead of 45s. And the ult should probably be 9 points.
As a hyper-aggro agent, his natural counter is simply to bait out his utility without much of your own, and then push back after he's exhausted his utility. For example, on defense, you'd have someone like Jett/Yoru/Omen show early presence, make him burn util on them, then escape and retake site while he has nothing.
In practice, the cooldown on missiles is low enough that he can use them both for site execs and for late defuse denial. He should be more like the Brimstone of initiators - powerful utility, but he has to choose much more wisely about when to use it or else he will just not have any left.