Hrm, this is a Maptools game and so far the players haven't picked up on any subtleties. Things that I thought would be obvious they seem to miss, like Kurychek who's tagging along with them 'cause they promised him the case once it's emptied. He's been spying on them and reporting back to Guthwulf. Kathor (who the PC's let live in the first encounter) warned them of this (I had him warn them of the Gauntlet ambush as a means to repay his debt) and they still haven't picked up on it.
Depends on whether you are okay continuing with a clueless party. Missing some XP, and seeing other consequences of their narrow-minded view, should wake them up to it. If you're okay with things as they are, though, and don't want to force them to understand the world around them, then your game shouldn't rely on subtlety. Spell it out for them and leave the choice of what to do with those facts up to them.
So the fact that she's oppressed and miserable, and enchanted even, probably won't be noticed unless I strongly hint at it. And even then, that'll just have them want to kill Haddin all the more.
Let them.
But she won't leave without Haddin...
If he's dead, I don't see Crystin choosing to remain alone at her collage. Even if he's not dead, she can be forcibly taken by the PCs. Again, the goal here, in my opinion, is to take Crystin with them, for two reasons: 1) Because the PCs should be saving her, and 2) Because she seems to have some sort of gift for fortune telling, and could be of use to the party.
Haddin is just a complication in all that. Crystin doesn't want to leave without him, and that's what makes the PC's situation interesting. Killing Haddin or simply kidnapping Crystin seem to be the immediate options for parties who really dislike Haddin.
But I suspect that your group, like my group, will allow him to tag along in any case. If they simply pass the two by, I'd make sure they understand the consequences of their actions. They don't get the XP, to begin with, but depending on how creative you want to get, you can do some interesting stuff. Have the news of Crystin's brutal slaying greet the PCs when they reach Seaquen, then have Haddin be one of the Inquisitors later on, his mind warped by his daughter's death, turning him completely into a Darth-Vader-like figure. Or have Crystin haunt the PCs dreams, relaying her prophecies to the PCs even in death, her torment costing the PCs healing surges after an extended rest.
Just tossing some ideas out there. I thought that Haddin and Crystin were some pretty interesting characters, as long as you allow the PCs to handle the situation in an unconventional manner.