I think there had to be SOME punishment for the gil, though. Depending on how Jarol feels about Karama, there may be a way to do it that won't permanently destroy his career. I hope she remembers how she felt when Gul Dukat and then Ahal tried to do that to her. Now, in HER case they were both absolutely wrong and had no right to do what they did to her.
Still, if Gil Karama is someone who can learn from what has happened, here's what I might do. I might find some way to punish him where it doesn't go into his file. Withholding the promotion is severe enough punishment, but if it's still early enough that she never submitted any paperwork, then no one ever has to know why she waited until later.
I think that Jarol is justified in not promoting Karama, though. From a military standpoint, Karama has demonstrated that he is unable to put the good of his mission (which of course in this case means not harassing the Federation officers) ahead of his personal problems. He had the option to either say to them something like, "I find the way you are treating me offensive, because it makes me feel like I've done something wrong when I never meant to," or if he wasn't comfortable talking to them alone, he could have told the glinns or Gul Jarol and asked for them to sit in on a meeting between them, to settle the matter. But I do think that an incident like this speaks to one's ability to handle a higher rank.
For the Federation officers, I think it will make an impression that Gul Jarol WAS concerned about what was happening, and that the standard for exemplary behavior includes NOT indulging in petty harassment and grievances.
As far as Jarol herself, I am glad to see that she is starting to really recognize that there are times when she needs to stop and let her head clear before she acts.
About the Skarrat situation...I think it will be hard to convince the Federation of what's happening there, especially when the genocide is found out. Jarol is probably making a serious mistake not putting that in the report, because I think even Alon Ghemor discovering it would be bad enough. Ghemor isn't a cruel man, but I would not be surprised if he fired Jarol for lying to him, if he felt she had proven his sense that he shouldn't trust her.
Oh...one more note about the humans. I wonder if now that she knows their memories don't work the way Cardassian ones do, she'll start thinking they're inferior?
We don't want her to learn the wrong lessons here.