Does this literally mean only 'What creature is eating Mara', or can it also mean 'what is bothering Mara,' as it does in English?
It canNOT mean "bothering" as in English, though I would guess the English sentence with the "bothering" sense is what inspired this Klingon sentence, even though it doesn't mean the same thing.
Only the literal meaning "devour, consume" of "eat".
For the metaphorical sense, you could say mara yIvtaH nuq meaning literally what is chewing on Mara? but yIv has the slang meaning of annoy, bother, irk.