Why would that necessarily be so? Even if the commander assumes the suspect is just a clueless idiot, there's still a chance he is a terrorist, so the same precautions are necessary.
Assuming something that almost certainly isn't true can never be a good strategy, can it? Thousands (maybe hundreds of thousands) of people try to break the airport security rules every day, mostly inadvertently; it just happened that this guy got through. None of those people are actual terrorists (some may be, but they have the day off), so shooting them in the head if they make a sudden move or don't immediately respond to orders barked at them might be overkill.
In essence, expect the best while preparing for the worst.
That's a commonly used phrase that is also a terrible strategy, well evidenced by our overreaction to the very minor threat of terrorism.
Of course, whatever any commander did would involve risk. Redeploying officers involves risking opening other avenues of incursion. Calling for an evacuation risks tipping off the suspect. The suspect might be using some kind of "dead man switch", so couldn't use a sniper, even if one was available. And a shit-ton more potential risks and other issues.
If you really were to assume everyone who violated security rules was a terrorist the sniper option is probably your best bet. There is almost no chance that they would have a dead man switch armed while simply strolling through the terminal, it's best just to silently take out anyone who walks the wrong way past a secure door or tries to smuggle more than 3 oz of liquid through the x-ray machine.