Why not just make him forget again?

Because it didn't work the first time; it only made things worse.

This is a recurring theme in both The Vampire Diaries and it's spin-off, The Originals: vampires using their powers to do "bad" things for "good" reasons, and how it rarely turns out well. In this case, Elena chose to use Damon's power to make a complex problem -- Jeremy's situation with Vicki -- disappear.

Unfortunately, the victims of these seemingly good deeds almost invariably find out, and they are never happy. They feel violated by people they thought they could trust. This is what happened with Jeremy, and it was made worse by the fact that the Salvatores were the ones almost entirely responsible for Vicki's drama.

Though Elena probably thought what she was doing was helping Jeremy, it would at least seem to him that she was motivated in large part by her desire to keep Stefan in her life. More to the point, however, her actions made it impossible for Jeremy to grieve properly -- to process his anger, sadness, denial, etc. and move past it.

Once all of that came back up, Elena likely realized she had made a mistake, and probably felt bad at her betrayal. Not bad enough to stop herself from doing it again in the future, mind you, but bad enough to hold back for at least a few episodes.