So I Was Watching Deathly Hallows Part 2

You know the part after Harry shows up in the Great Hall and McGonagall "fights" Snape (I put it in quotes because all he really does is throw a few shield spells and fly out the window)? And then Voldemort talks in everyone's head and demands that they give him Harry Potter. And Pansy says, "What are you waiting for? Someone grab him!" And then Filch comes in shouting about students out of bed and McGonagall says his arrival is opportune. She says, "Please escort Miss Parkinson and the other Slytherins out of the Great Hall...the dungeons'll do."

So anyway, I was thinking about this and it seems horribly unfair. I mean, throughout the books, J.K. Rowling talks about how not all Slytherins are evil or bad. But rather cunning and, if anything, usually out for themselves. But that doesn't make them evil. And I felt like, when McGonagall sent all the Slytherins to the dungeons because of one, well it was horribly unfair. Granted, on a realistic level, it probably made their battle easier as, I'm sure, a number of the Slytherins were, or would've done, sided with Voldemort. I just found it to be against the principles usually put forth in the series (books and movies).
But again, that's just what I think. And I wouldn't really worry about it if it seemed that there was a reason for doing so, such as the Slytherins needing to be in a certain place for something else to happen later on. The only thing I can think of is that Draco, Goyle and Zabini apparate from the dungeons to the Room of Requirement to intercept the trio. Also, I just realized this, I thought you couldn't apparate in Hogwarts. I suppose Snape or the Carrows could have removed this for some reason but that doesn't make much sense. Plus, the teachers had been placing protective enchantments for a while by this point and I think that would have been one of them (if not already in place).
Back to the original point, however, this moment here is the only time we see the Slytherins in relation to the dungeons. Then, this scene isn't even in the movie, really. It's in the deleted scenes.
So was there a reason for sending all the Slytherins to the dungeons? If you have any ideas, let me know. Or if you think I'm reading way too much into this, keep that to yourself. Just kidding, tell me that too.
Love you and, as always, thanks for reading!
-Alyssa