She didn't bother me as much as she seems to bother other people. She's clearly very intelligent, and for me, her threat wasn't any kind of actual intention of harm towards the IQ as much as it was a confession that she still cares deeply about Varric and what happens to him.
That said, I definitely think they are hurting themselves, and each other, by clinging to their relationship. She very obviously did not want to marry the guy she got arranged to be with, and I can sympathise with that - it's a sucky position to be in. But one way or the other, they have both made their choices now. It's not really ok to be sneaking out on her husband - he may not have any expectation of faithfulness, given that it seems to be more of a business/status arrangement, but it does endanger Varric, and her. And he deserves a chance at a real relationship and a real life, not whatever crumbs she can throw to him every few years.
If she really wants to be with him, she needs to be willing to break out of the forced marriage and commit to Varric, and damn the consequences. Certainly I think a lot of ordinary people on the surface, at least, would be willing to grant some leniency to her given that she already tried to get out of the marriage once and is in it without her full consent. But if she can't or won't risk that, then she needs to let Varric go and move on, for both their sakes.