Everyone is/was aware of Hillary’s crimes (i.e. illegal server, deleting emails under subpoena) those are facts. Ilhan Omar’s crimes are not yet widely known. Once they are and she’s being prosecuted, he does not want to be accused of a witch hung (i.e. prosecuting her for purely political reasons). Real simple. I’ll trust Trump’s instincts over yours any day.
Omar will be fined ( as she has already been for some of her crimes )and allowed to "update"/change some of her past fraud; however, I have grave doubts that anything else will happen to her.
I doubt that this apology was Trump's idea. I bet someone got his ear and convinced him to do it; unfortunately.