Hi,
Regarding FITS, it can be removed, yes. The implication will be that any format without an existing rule for file characterisation with a more specific tool (Mediainfo, Exiftool, etc) will not be characterized (FITS is the "fallback"). However, a number of our users remove or disable FITS anyway because they find its verbose output is too much of a performance hit so it may be a win-win for you anyway.
The jquery question is beyond my knowledge, apologies- I'll see if someone else from our team can respond.
Cheers,
Sarah