fill up does not have any suitable meanings in this context: you might, however, say "to fill the gaps in the existing code of conduct".
address and cover are both appropriate in this context. mention implies that not much detail is provided, whereas address and cover both suggest a complete solution to a problem: it might be a good idea to use one of these words to replace mention as well.
mention - to speak about something quickly, giving little detail or using few words
address - to give attention to or deal with a matter or problem
cover - to deal with or direct attention to something
come up with sounds quite informal, and suggests something that might be temporary or inappropriate. devise is more formal, and would suggest that some serious thought has gone into the new guidelines. You could also replace established with existing.
counteract and balance out suggest that you are adding something that directly opposes something that is already there- a minus to counteract a plus. In this case, you are adding something to fill a whole where there is corrently nothing. You cannot counteract or balance out something that isn't there.
deal with is certainly a suitable alternative: as you see, it occurs in the definitions of both cover and address.
I would therefore modify the sentence to something like one of these:
The company has to devise a new set of guidelines or rules to address what is not covered by the existing code of conduct.
The company has to devise a new set of guidelines or rules to fill the gaps in the existing code of conduct.
The company has to devise a new set of guidelines or rules to deal with the gaps in the existing code of conduct.