Is the conflict going to affect either your job or research? I understand you can't go into details but a PhD student shouldn't have any major conflicts of interest that can't be easily resolved. Unless your jobs requires you to have an active business relationship with a part of the university I doubt anyone will care. Though it is generally is it better to declare a conflict upfront; as in politics, the allegation of covering up a conflict is usually worse than the actual misdemeanour
Also, listing your employer in the affiliations shouldn't be a major issue and I have seen several journal articles were an author is affiliated to both a university and a company.