hmm... i guess, your Mac is out of warranty. if so, there is absolutely nothing, what can stop you from reapplying the thermal compound. yes, apple computers, especially their MB looks like someone have used spoon, when applying... too much and at wrong places. if you get thermal compound, try to get silver one. it is the best.
maybe your heat-sink is clogged again. try to clean it. maybe the fans are not working. did you try any sort of monitoring application, to check on fan RPM's?