Detection spells, like the one used on Harry to detect him despite being in his invisibility cloak. Not much use being stealthy when everyone knows were you are no problem. This basically devolves into a normal battle (as normal as this can get anyways).
The ninjas get a good amount of kills, but the teachers and the more skilled students eventually take them.
Hogwarts has spells like Protego Maxima, which is basically a barrier that causes all spells to bounce off and anything solid to disintegrate instantly (bodies, shurikens). One of those casted around the school already makes this a stalemate, and there are two professors at the school who know how to cast it.
Stupify is an instant knockout, and even the weakest students know it.
There are a ton of defensive spells and a ton of offensive spells. That combined with all the secret chambers, and ins/outs gives the witches/wizards a massive homefield advantage. You said they have to kidnap harry? Have him hide in one of the many magical rooms they cant enter, and it's already mission failed. Hogwarts wins.