Perhaps, but I suspect it then lies with a difference between why the player's making the choice and the choice we're actually providing them. At no point is the choice "kill Isabela" offered, just as at no point is the choice "kill Leliana" offered. If someone thought the Qunari would kill Isabela, that's fine, but the fact they didn't doesn't change the fact that the choice was to turn over the person they wanted in order to get a peaceful resolution with the Qunari... which you actually got.
Thus saying "my choices don't matter" is like a shorthand for "what I wanted to happen didn't happen"... which is fine, as folks will want what they want, but I'm afraid you're not going to get much more than a shrug from the writers.
Understandable, but I've always found it a line that's a bit difficult when it comes to crossing. Kind of like DMing a P&P game, really. It's a bit of a pain to balance "What we want to happen", "What they think will happen", and "What actually happens" when it comes to choices.
The problem is that people can - and sometimes will - resent it if they feel like they're just being railroaded.
- DAO did a rather good job at avoiding this, except with that Leliana choice. Connor's fate is actually in your hands. As is Alistair, Anora, or Loghain's. Or any number of people. Or even "lesser" choices, like in Awakening with the trials. It doesn't always have to be life-or-death.
- In DA2, you feel more like a bystander than anything else, because so much is never in your control. That's part of the point, granted - Hawke isn't exactly the force for change the Warden is - but that game has a lot of false choices. You are led around by the nose more often than not, and there's not a great deal of deviation.