1)
I think " 。" is a typo of " 、".
2)
It's supposed to mean 誰かが大ビーカーになみなみと入れた『骨生え薬』を飲ませたばかり, as you interpreted correctly. Actually, this sentence grammatically can't mean so (i.e., incorrect and not-make-sense as a Japanese sentence), and is pointed out that one of the worst mistranslation of this translator.
3)
Yes, 先生方 is the subject.
4) a)
It's an ironical use of 憎い, meaning "excellent / admirable / graceful".
b)
あまりの means "extremely". あまりのことに is used as what has happened is extremely bad/good for Flitwick.
5)
It's close to "Come on!", "Oh no!" or "No kidding!".