I wanted to be an Independent Courier and spare Ulysses' life. Throughout the DLC I've done my good deeds like saving ED-E. But I just beat the DLC and I was FORCED to kill Ulysses (I literally tried 5 different times to see if I could get him to comply so I don't have to kill him.) I still have a save to revert to, but I don't want the game to end like that. It's not SUPPOSED to end that way! We were supposed to be best buddies. I also got Ulysses' Duster and my Vegas Duster. (I have best rep with House.)

So, I do I HAVE to kill him? I like his stalkery tendencies.

I think you can use the tapes you find throughout LR against him, then he stands down

You have to make the correct dialog choices in order to spare Ulysses, refusing to nuke any party shouldn't matter.