Look it isn't hard to see how it is:
1. Jaina isn't evil. She just lost all confidance in the horde. Something I think she should have gotten rid of a long time ago. Sure she had a good experience with the horde. Hell I thought that WoW itself was flawed from the start because the horde and the alliance were very good friends through Jaina and Thrall through WCIII. So I saw no reason to start a war in the first place. And I thought she was very levelheaded when they killed her father. Something I did not truly understand. How can you stand there and let your father be killed unless you hated his guts in the first place?
Anyway after Theramor was bombed, she still wanted some form of peace right? She was mad but not as mad as when the horde betrayed her in Dalaran (mad=angry). And well who can possibly be angry at Jaina afterall she had gone through? I am sure that if Thrall would have been Warchief, she would still be the happy little BORING mage we knew for years. Now she finally woke the fuck up. And while I still understand her rage towards the horde, imo this should lessen over time. She will probably always be cautious about the horde from now on. And I think that is very healthy concerning her dealings with the horde sofar.
2. Or Blizzard wants to do a 180 on this character and indeed turn her into a raidboss. When this will be is obviously undetermined. But I think it would be a sad day to get rid of her just because she just got real. Instead of a passive very understanding almost horde loving alliance leader. She is (afaik) one of the last links to WCIII and Arthas's story apart from Sylvannas. This is not Game of Thrones where everyone needs to die imo.