I'm sure that she's a little bummed about the mixed reviews of Monday's show, but she and Colbert have a relationship. I really doubt that Colbert would go to the point of genuinely insulting Rachel, and she certainly seems to have enough of a sense of humor about herself to take it. I didn't think it was a swipe as much as an ironic "touche" of sorts. In the greater scheme of things, she might even see the entire episode as a bit of a win. She got over 4 million viewers and, for those that aren't regular viewers and/or political junkies, the context, especially about the Russian oligarchs, may have been welcome.
I do wonder about the choice to go on air, etc. Johnston, after all, was the one who received the returns, which he also disseminated on The Daily Beast. It is possible that he oversold the story and MSNBC/Rachel erred in building up the pre-show hype.