first off the BOS are not automatically good guys. Previous games left it to you to decide either they are your friends or not or even how they operate (FO:T). But they are enemies of NCR...
If you put Hardin in charge I don't know how you can make peace between NCR and BOS either. They do make it easy to eliminate them though
Spoiler go in and rig the reactor to blow up
otherwise if you are on the side of the NCR you are stuck doing their dirty work...sorry. Just remember that in the FO Universe The Brotherhood are not as noble as they claim to be and after a long bloody war with the NCR the chapter you are gonna wipe out are basically terrorists in the eyes of the NCR.