Wide area stun is such a nifty tool that the failure to use it in every episode warrants an explanation. And it's not difficult to come up with one: after all, we know that stun kills.
With a bunch of burly gangsters all in the open without protection, this is not a problem. But the intoxicated McCoy might not survive stun, while most enemies would be protecting themselves so that the stun would just kill the cute little babies and puppies before managing to stun the enemy troopers.
Of course "City" is also a special case in that the timey-wimey anomaly of the week messes up pretty much everything (except for the transporters - a rare event indeed!). If the ship can't even fly straight, could Kirk trust her to shoot straight? Or to locate McCoy before he choked in his own vomit?
It is also a bit doubtful whether firing the ship's guns straight at the mysterious anomaly really is a good idea...
Timo Saloniemi