Maybe she should, but it’s in Elena’s nature to forgive people no matter how heinous their crimes are. If she held grudges she could never hang out with vampires. She forgave Damon for snapping Jeremy’s neck, which was just as personal and devastating as Stefan driving her over Wickery Bridge. She befriends vamps like Elijah, who have a millenium of darkness to account for. She’s the opposite of Bonnie in that sense, who clearly sees where the lines are drawn in the sand.
Here’s the other key point: Stefan is going to hold the Wickery Bridge mistake against himself forever. He doesn’t need any help from Elena on that count. It is consistent with Elena’s character for her to forgive him and try to move on, but Stefan won’t forgive himself and won’t let himself move on, because that’s the way he rolls. And actually, that very stubbornness is what’s so detrimental to his character: it forces him to remain stagnant.
If, as an audience, we care about Stefan healing and becoming whole again, we shouldn’t be in the business of holding his deeds against him forever. He’s doing that well enough already. Until Stefan faces his guilt and pain and is able to move through it, he will never be able to turn a new page. He needs to forgive himself.
I’ve said it before and I’ll say it again: forgiveness is a big theme in The Vampire Diaries. Keeping this theme in mind, do you notice how Stefan has not yet apologized to Elena for how he’s hurt her? Even in 3x12 he says “I shouldn’t have kidnapped you,” not “I’m sorry for kidnapping you.” Why? Because he doesn’t want her forgiveness. That’s how much the dude hates himself.