You are not allowed to ignore a companion quest in DA2. I tried to not do Merrill's quest because I didn't want the Dalish to die and I didn't want her to go down that path and the game would not allow me to go into the Deep Roads until I had completed that quest.
You have to recruit every companion in that game. The game does not allow to you deviate.
Untrue - I've played the game without Fenris or Isabela, and after doing the Act 1 quest with taking Flemeth's talisman (and wow, talk about a character who has plot armor), you can tell Merrill you're not going to see her again and she doesn't become a companion. Anders you can send away after Dissent (although he does come back at the end,) you can ignore Sebastian's quests and not recruit him, and obviously you can let both your siblings die in the Deep Roads. The only companions that you can't get rid of at some point are Varric and Aveline, and I've heard that even Aveline can be sent away before the end with certain choices.
She's one character and one that the player should have had the opportunity to kill/imprison for her crimes. Limiting this choice and forcing her upon a person role-playing a diplomatic character who believes in justice isn't a good design concept for a role-playing game which allows you to bring justice (or non-justice in Fenris' case) to other companions.
You can skip recruiting Isabella completely but if you do recruit her and learn of her involvement with the Qunari, you have to have high rival/friendship with her to even get her to show again to hand her over to the Qunari. The OP is hoping that in Inquisition, we get the opportunity to kill her or turn her over to the Qunari again who can successfully keep hold of her this time. Point being, the OP, like I, wants to be able to bring justice to Isabella.
...and let's not even go into detail over how many people she's infected with STD's (a crime within itself).
You stole the Qun, the holy relic of the Qunari, sparking an uprising costing the lives of thousands when you had the opportunity to avert this, you bumped into the Arishock who now has to be washed and sterilized and so you go to prison. You lose! Good day sir!
Why is the fact that she had some mild sex-related disease (probably crabs, something that's really common even in the world today, and no, it's not a crime) make her someone so dirty that anyone who touches her has to be sterilized? You do remember that the way we find out about her hilarious infection is that she's going to the healer to get herself cured, right? The fact that she got herself treated for it speaks to a far greater sense of responsibility than a lot of dudes have when they find out they have an STD.
I'm sure you were trying to make a really funny joke, but considering that it's a joke that literally everyone makes about any woman who's shown to partake and enjoy promiscuity, it's falling pretty flat. It also implies that her promiscuity is part of what makes her a bad person.