They're also not troops she's leading; they're just civilians, routinely being charged with holding the kingdom together.
You'd explode Rainbow Dash? Are the Wonderbolts ever explicitly referred to as military? I'm not saying they aren't, I just can't remember.
They were started as a military group dedicated to protecting Celestia, and eventually became known for their aerial feats. They're sorta like the Blue Angels or the Thunderbirds, except for the fact that they apparently actively patrol Equestria.
Fair enough; Dash has always been the most militant and martial of the group. The inconsistency of the group's power annoys me sometimes though; I mean, they've defeated some of the biggest threats to Equestria, but then are given trouble by the likes of Starlight Glimmer and Ahuizotl? I guess ultimately it's just a kids show, doesn't need to make total sense.
When they went up against Starlight Glimmer, they were basically going in blind. They had no idea what she was really capable of, and once she got the drop on them, there was little they could do to fight back without hurting the innocent townsponies. As for Ahuizotl, the extent of his power isn't well defined, but he was shown to be extremely intelligent and ruthless, and had the ability to control big cats like tigers and panthers... more innocent creatures that the Mane Six had to avoid hurting. Plus, they fought him at a time when they'd been disconnected from their Elements of Harmony.
They're disconnected from their Elements when they fight through an enormous crowd of changelings, and they seem to have no trouble then.
That's because the Changelings were weak and starving. Why else would Chrysalis have been desperate enough to openly attack Canterlot?