I don't think it's anything to really be dealt with, unless you object to the idea of torture in your games. Of course, there are detriments to using torture, which is why it's a case of last resort (or no resort) for many intelligence agencies. What detriments?
- People will say anything to get out of pain. You end up with a lot of dross to sort through, especially when someone doesn't really know anything.
- If word gets out about what's being done, their enemies will react a lot differently (fight to the death, fight harder). Their friends will, too.
- Torture doesn't work on pathological liars.
So, if you want to introduce the negative consequences of their actions, I'd suggest the following regimen:
- Have them get erroneous information from the torture, that really bollixes up the investigation.
- Have their enemies find out, and use that against them in bonuses to their morale against the PCs/Bonuses to attack.
- News agencies. In modern times, if news of this gets out, there will be ramifications (see Abu Ghraib and Gitmo)
- A variation on 1 - get a lot of information, some correct and some not. It will still take investigation to untangle.
Personally, I don't limit most things in games- but I do try to play the ramifications of the PCs actions- both positive and negative. In many (most) cases, these ramifications are enough to make the PCs take a hard look at their actions, if not change them.
(you might want to look at the question How do I get My PCs to not be a bunch of murderous cretinsHow do I get My PCs to not be a bunch of murderous cretins)