There should be potential negative consequences for doing the "bad" things as well as the "good" things, if doing good is going to cause bad things to happen. But in general, in Dragon Age, doing good things takes more effort. In DA:O you could also decline rewards, doing good deeds out of the goodness of your heart, but if you decline a reward, don't expect anyone to give it to you anyway. So I don't really see an issue; if you go the extra mile to find that better solution, then the better solution should have a good chance of working out.
Others are right, too. I played a very good-hearted Hawke in DA2, and it felt like the game just stomped on my goodness. So I don't want that. Doing good deeds shouldn't be treated like it's a stupid thing to do. And in all honesty, I'd rather the kinder decisions have greater long-term rewards than the cruel ones. But maybe that's just me.
Don't get me wrong, I like George R.R. Martin quite well, but I don't think all fantasy should be quite so grim. Doing good deeds shouldn't result in automatic failure, and being ruthless should only have good results if there's no other sensible option.
Or, it could take a different tone, and the more ruthless you are, the better your outcomes get from being ruthless. The more merciful and good you are, the better your outcomes are for being merciful and good. That would make the most sense to me, without making players suffer for their preferred style of roleplaying through the game.