The virus idea is a good one, but I wonder if what happened on Miranda might make them think twice. Not forever, but it might be one reason why the Alliance hasn't done anything like that. Also, like the original poster said, they do see themselves as the good guys.
So, maybe they figure Miranda was a good idea, but done poorly. Luckily, there are plenty of other planets on which to try it out, keep at it until it works. If the PCs happen to be on one of those planets, or intercept information about it, that could set them on the trail. Or it happens to a planet to which they have ties, and they arrive after the virus has burned itself out, but not before the new Reavers (or whatever the new test creates) finish their work planetside.
And again, there's always creating a false threat in order to make people turn to the Alliance for protection. The Reavers might be a tool they could use, but that threat exists, and no one is screaming to the Alliance for help. It would have to be substantial. Heck, it might even be real. What about a theat that actually exists, like a comet or asteroid on a direct course for one of the more populous outer rim colonies? Who else could help but the Alliance? And what would be their price?