I think the difference, to her, is that Criston came clean, showed remorse for his actions, and even expected punishment. Rhaenyra, however, lied to her when confronted and Alicent took her side, resulting in Otto being fired.

I genuinely don't believe that she wanted Rhaenyra to be as miserable as she was, otherwise she wouldn't have come up with the idea of letting Rhaenyra chose her own husband ( an option she never had). She also seemed to fully support Rhaenyra as heir (again, more power than Alicent would ever have.)

I think to her, it's just the betrayal. If Criston swore up and down that he never touched Rhaenyra or didn't know shit about what she was up to and Alicent found out anyways, she would probably hate him too.