Here's a few potential ideas:
1) Parent organization finally cracks down on them (they went too far? tortured a relative of someone important? under new management?)
2) New enemy that looks normal but is actually an imprisoned demon/alien/whatever (or they have a berserk Mr. Hyde personality), torturing the host releases it to try to kick the party's butt
3) Fake teeth with poison in them for committing suicide become wildly popular (or better yet, an implanted bomb they can detonate by thinking or saying trigger phrases; they not only deny the party information but also potentially kill the torturer)
4) Characters are afflicted with a disease / curse / alien implant that causes them to suffer harm when they torture someone
5) People possessed by something that makes them outright immune to pain
6) FBI or some other normal government organization without clearance to know about the party starts investigating all these kidnap/torture murders (possibly leading to pressure from party's parent organization to cut it out, per #1? Alternately, parent organization might even decide they're a risk and cut them loose to fend for themselves)
7) Families of tortured people realize some shadowy group is doing this (but don't know about the paranormal stuff), band together to hunt down party & avenge their relatives
8) Party is haunted by ghosts of their victims, who interfere when the party tries to do anything (penalty to certain rolls?)
9) Party fights an angel or other creature of judgement, which gains power for each person they've unjustly harmed
10) Nail them with any alignment penalties the system happens to have
11) Create new alignment penalties as they become corrupted by demons (check out 2nd edition D&D's Dark Powers checks from the Ravenloft setting: get noticed by the dark powers too many times and your character turns into a being of pure evil and becomes an NPC super-villain)
12) Combine the above, so that each time (or even just most of the time) they try to use torture, they run into some new problem
Instead of all the above, you might also try to talk to the players. Explain you think it's getting a little out of hand (is anyone uncomfortable with all this torture/murder? have them speak up!), and ask them to tone it down a bit.