Maggie Sawyer made a mistake. She was embarrassed and ashamed. She didn’t want Alex to find out because she loves her and wants to be better for her. She was not doing this for her own personal gain, she wants to be the best she can to Alex because that’s what she deserves. She felt guilty and wanted to atone for her choices so that she could move on and give her whole heart and trust to the woman she loves. Maggie Sawyer does not expect forgiveness, she does not expect Alex to react the way she did because it was her mistake and in her mind it was unforgivable.
Mon el lied to Kara fully expecting that she would forgive him. “This is usually the part where the girl forgives the guy for whatever stupid thing he did.” Mon el didn’t care to think how the lie would affect Kara, he actively covered this up because he knew that Kara did not agree with the Daxamite royal family and he didn’t want to ruin his chances at getting the girl. He didn’t lie to spare her feelings, he lied to keep himself in the running. Unlike Maggie, he had no fear of ruining the relationship because he figured that’s what Kara does, forgives and forgets. He figures if he convinces her that he’s trying to change (even if he doesn’t make any actual effort to be a hero and to make change in Daxam, the place that he owes it to) that she’ll pity him and take him back.
The relationship here has been set up that Kara is now reliant on Mon. She has been conditioned to feel guilt whenever Mon el runs astray. Whenever he makes a mistake she feels responsible because she is trying to reconcile what she couldn’t do with Kal. She stays with him because she feels responsible for fixing him. The problem is, he puts no effort into fixing himself.
With Maggie and Alex, both are trying to be better for the other, both are actively supporting and defending each other when the other is struggling. Both are respectful of each other and actively involve themselves in each other’s lives, the good and the bad parts. They are both putting so much effort into their relationship and into bettering themselves individually.
What Maggie did to Emily was wrong, what Mon El did while ruling Daxam was wrong. The difference is that Maggie feels this guilt and actively tries to rectify this, not expecting anything for herself but wanting to give Alex the love story that she deserves. Mon el does not show any guilt and expects forgiveness regardless of his lack of effort to rectify his mistakes both on Earth and on Daxam.
What Maggie did and what Mon El constantly does are not the same thing.