Well, now that I think about it...
-The whole magic world armies is weaker than any single member of Negi's team as seen on the last battles. And don't give me that "oh they're magic world citizens so they auto-lose" crap, when Negi's crew was on the magic-created battleship it blew up demons just fine!
-Their best security system was broken down in a matter of seconds.
-Dragons, suposedly the biggest most fearsome beasts around, are little more than chump fodder for even the suposedly weakest Negi members. Nevermind the ninja, Yue defeated one with a freaking knife!
Trained by the Dark Evangel.
Evangeline noted that they'd be capable of dealing with anything short of a full army when they left, and being separated was power leveling for them.
The armies CAN hurt the enemy forces, but only if 'real' people are on board. Godel said as much, real people can hurt them, magic world people can't. It's not the weapons, it's the motive force for them.
The security system is not actually defeated by Chisame's skill, it's defeated by the artifact Negi spawned + her skill. More the artifact really, and by extension, Negi.
The dragon didn't lose to a knife, it got hit by an attack with a powerful lightning spell on it's weak spot. White Lightning is, remember, as powerful as Mahora Festival Negi could pull off. So assuming it's the same grade of dragon in the school basement(unlikely, the griffin dragon seems weaker), Setsuna noted she could have fought it if she had the time.
As for the artifact matter, it was noted that only powerful mages/ki users grant them at all, and as we've seen, Misora's artifact(super running shoes) is nowhere near the same tier as Negi's harem's. So you need a certain minimum power to grant an artifact at all, and the ministra needs a certain level of trust(Negi can for example, summon any of his girls to him within a certain range), and if the ministra doesn't have enough energy to power the artifact, all that power comes out of the mage.
If Negi wasn't protagonist material he'd have fainted from the mana loss of supporting so many contract activations.