"Sorry, you're not my type" or "I'm not interested in you in that way, sorry. Can we still be friends?" should be options as friendly let downs for companions.
I agree there should be friendly options too.
Which companions have the 'flirt or be mean' options again? I was just talking to Vector with my one Agent and it seems like I can just easily avoid flirts and pick "nice" dialog (but then again he doesn't flirt with you).
I think Doc has one like that (you get 2 options that are flirts or you can reject him not so nicely)....I'm trying to think of some others. I don't play male PCs so I don't know about female companions.