I'm not a fan of the Qun. The fact that Bull becoming Tal-Vashoth ties in neatly with saving the Chargers makes me very happy, I must admit.
A Qun-following LI would take lots of getting used to for me. If they try to proselytize, then that would be a deal-breaker.
Thinking about Sebastian, I will say that his faith was not one of my issues with him. In fact, I thought the writers did an excellent job. I didn't find him annoying for his faith, nor all that preachy. He was alright there. I think the writers can work with this Qun idea.
Personal complaint about a Qun LI: We've had a DLC and now a full game with current/former members of the Qun, and I still can't ask about mages. Why some Qunari think that "demons ride a mage's very words," and others seem more laid back. I'd like to be able to question the next Qunari that enters there party about the differences. The different ranks of the Qun seem to hold different viewpoints on some issues than the rest. It would also give the players a chance to see more of the complexities of the Qun, and where love can fit into all of this.
Personally, I can see a Qun KISA type bending the rules when it comes to sex, if the player should so choose. It would be interesting to have a Qunari that's apart of the Qun less open than Bull, but more world aware than Sten.
Boy, I'm getting all sorts of picky today. I guess it's the Well my character drank. Coffee and off to finish the game with my warrior. 
Edit: Not a Qun fan either, and I agree about Bull and the Chargers. Felt good to watch them walk away back to Skyhold.