Momentarily B'Elanna was the Fourth Officer and Chief Engineer. Unlikely as it seems, for a while there she was one gas leak away from being Captain, and all the while she was quite publicly dating a mere
Ensign. Before that, Ensign Vorrik saw no issues whatsoever in proposing a strenuous and medicinal sexual relationship with the same girl who was his direct commanding officer, without registering the slightest a single impropriety about the question. Meanwhile lowly Ensign Seska tried to sell her naked rights to Chakotay without much success.
Kathryn is a Prude, whatever rules were in place could obviously be bent into a pretzel if a "couple" was invested enough and bloody mad for each other. Considering how brazenly this Captain defied the Prime Directive time after time, it's amazing that she would notice a tiny rule in the periphery asking her to keep her knickers on in mixed company.
Was Neelix outside the chain of command? Whatever rules stopped her from boffing crew, wouldn't have applied to Neelix or Icheb or the Doctor(?No rules against frakking lightbulbs.) and shouldn't have applied to the maquis since they were not real Starfleet Officers at all but just convenient slave labour.