Why wouldn’t Stefan protect Elena? He has been doing nothing but since he saved her life in the car accident that killed her parents. Klaus will find out eventually that Elena is alive, yes, but Stefan will do everything that he possibly can to keep Elena safe and under the radar for as long as possible.
I’m getting the feeling that quite a few people were upset that Stefan told Elena to stop, to give up, that he didn’t want to be with her anymore, but I am not upset in the slightest. He said all of that to get her to leave him alone, to stop looking for him, because that is what’s going to keep her safe. He did it because he still loves her and he absolutely does still care about her. There is no doubt in my mind about that.
This season has really made me appreciate what Stefan and Elena had. Seeing Ripper!Stefan in the flashbacks, where he was completely psychotic and just didn’t give a hoot … it truly shines a new light on just how amazing the Stefan that we have come to know is. He’s been “clean” if you will for quite a few years (with the exception of the past few months, of course), but from what I understand and have seen so far, he wasn’t really alive during his latest clean period; he wasn’t engaged in life. Elena brought him to life, she got him to feel and love and laugh again, she brought the absolute best out of him, she’s the one who ultimately saved him from a life of feeling nothing. Elena IS his lifeline. You cannot convince me otherwise, and you cannot tell me that they won’t find each other again, and I don’t mean literally.
Like I said, getting to know Stefan’s history has, if anything, strengthened my complete faith and adoration of not only Stefan, but Stefan’s relationship with Elena. It is one of the most beautiful relationships I have seen portrayed on screen, and all that I mentioned above about Stefan’s evolution and his relationship with Elena… of course he would do absolutely anything to prolong her safety/life.
I hope this answered your question? I can get off topic sometimes. I’m too invested into these characters/plot. :P