I think her greatest fear - which may have already happened in canon, and certainly has in my story - is being forced to kill someone she loves. I think Loki came close but had it the other way around, that it was being killed by someone she loves.

My imaginary canon that I couldn't get into the story is that when Clint was sent after her, without really being conscious of it, he gave her enough openings that she easily could have killed him. It was his equivalent of Selvig putting a kill switch into the doomsday thing - his subconscious trying to do the right thing. And Natasha noticed.

But she will never tell Clint, because she knows that no matter how much you trust someone, they can be brainwashed or tortured and betray you without ever intending to. The last thing she wants is for yet another sadistic supervillain to put her in a kill-or-be-killed situation with a friend. Also, if Clint knew that he nearly did make her worst fear come true, it would only make him feel guilty. Guiltier.