Isabela was my Hawke's love interest as well. However, I would say that she is one manipulative and self-centered pirate wench. That is something you have to learn to accept / like / tolerate.
She does remind me of...strike that...she is the female version of Captain Jack Sparrow...I mean if you take Jack, turn him into a woman, remove the weird walking thing and you essentially get Isabela. Both are good swordsmen, both copulate a lot, both drink a lot, both are willing to do anything to get a ship and both have some form of compassion deep down.
As for her not having to pay for her crimes, I am not exactly all up in arms about it. Be it Isabela or Petrice or Loghain or Howe, the whole "people did a great deal of wrong and they have to pay for it in some way !" is a manifestation of karmic beliefs and/or "an eye for an eye" from the Bible. It is, IMO, a manifestation out of the fear that our actions don't really matter on a grand scale / scheme of things or it is a reaction to the unfairness of life.
Sure, there people did mess up the lives of others very badly but the reality is, we live in an indifferent universe does not actually give much of a damn about morality and consequences of moral actions / immoral actions. Sometimes they get what is coming to them, sometimes they do not, sometimes we get to have a say in that, sometimes we don't. That is just reality.
Bottom line is, if you dislike Isabela and feel that she has to pay for what she did, then by all means, make her life miserable. You are entitled to that course of action. You can give her away to the Arishok if you wish. However, this is a dynamic world and expecting Isabela to not react to that is quite foolish.
As for Isabela being promiscuous and ridden with STDs, this is Thedas, not Earth. They have magic and we here might, in the future, come up with some genetic / nanotech treatment that renders STDs powerless. In Thedas, a sufficiently skilled healer can essentially bring back someone from the dead with a Revive spell and heal groups of people in one go with a Group Heal spell. As such, curing someone completely of STDs, especially by a Spirit Healer, is quite frankly, a common thing there.