After beating the DG MQ and getting bored doing the radiant quests to get the Rune Axe I finally told Serana to cure herself. Note I hadn't been using her for a while now and she had been hanging out at the castle. When I did talk to her before she always had the option to join me, however when she came back (note she looks the same, orange eyes) she now doesn't have the option to join anymore. I really wasn't planning on using her but thought it odd that she won't be a follower anymore.

Is this the way it is supposed to work or is this a bug?

No one is certain. At some random point for different people, you lose the dialogue options to have her rejoin you after either dismissing her, or giving her the 'wait' command. I suspect it is a bug due to that last one, plus it isn't 'in character' for her if you follow a certain dialogue path through the dg mq.

I don't know if it's permanent (I suspect it is), and the only solution so far is to go back to a previous save and not have her leave your side at all, for whatever reason, if you want to keep her.