Manga is most definately an Art, and those teachers should be slapped for their ridiculous, ignorant comments and their discouraging a student like that. However, I can't say they were wrong in making her create a different piece without seeing her work as a manga artist.
The thing is that there are many manga and anime fans out there today, and as much as I hate to have to say this, many of them THINK they can draw manga very well, when they really, genuinely suck at it. Kind encouragement from friends don't help in this situation.
I, myself, am an A-level art student who choose Manga as the style for my coursework project. My art teacher was hesitant at first about letting me use manga as my style, but I showed her some of my works and she decided to let me go ahead with it. In last years AS results, I got an 'A' in my coursework, where I combined manga styles with oil paint. At the same time, a GCSE student (possibly inspired by me :P) began doing her work based on manga also, combining manga with acrylic paint. She ended up getting an 'F'... (To be fair, I've never done GCSE art, so i don't know if the mark scheme is different or anything.)
But here's where my above stated point comes in; all her friends tell her 'oh my god, your manga art is amazing!', 'wow i wish i could draw as well as you!'. But when I peaked at her work, her manga art was really average. in fact, it was only boarderlining average. (i feel awful for saying this, but it's sadly true -_-)
Our art teacher disapproved of her using manga style even though she had encouraged me. And I hope i don't sound arrogant or up-myself when i say this, but in all honesty, my teacher was right in the sense that using this style wouldn't get the GCSE student high marks like it would for me.
For your particular case, judging by the teachers' nasty attitudes, I'd probably blame their stupid biased views rather than doubt your friend's artistic talent, but I think it's worth keeping in mind what i'm trying to point out.
It is very important to do what you're good at though, if manga is what your friend is really good at.
example time! In my exam piece, I thought i'd try something completely different, unrelated to manga. (i used collaging, mixed media and stuff like that) and I got a C. ^^" Proves that you have to stick with what you love, and do best at, doesn't it? xD