For all we know, that prisoner you showed mercy to could end up discovering a new way to fight demons. Much like Alec the farmer will turn into Sir Alec, founder of an order of knights that will last for a thousand years.
The moral comparison between Loghain and Isabela isn't even remotely the same.
Loghain willfully commits atrocities that could have been avoided, and makes devastatingly bad decisions. He makes it very personal for my character, including assassination attempts and torture. That's not even counting the Human Noble and City Elf problems.
Isabela? She stole the relic and then....lied. Played dumb about the whole relic thing. It was foolish of her to not tell Hawke, because Hawke could have dealt with Castillon easily, and then negotiated with the Arishok. And yes, lives were lost. She bears responsibility, but not all of it. Petrice takes up a large chunk of the loss of life, as does Aveline, who pressed the issue by demanding the Arishok turn over those converts. And let's not forget the Qunari themselves, who did the killing. They should have thought like bas and checked the Hanged Man. Obvious place for a thief, really.
Isabela is greedy, but she's being coerced. And she turns around on her own accord. That's worth something. As the Arishok would not surrender those under his command, neither would I.
EDIT: Doesn't surprise me Cauthrien isn't tracked. Still, I could imagine her having a good story arc.