No. Sudden temperature changes are not good for computers (worse than the heat you are experiencing). They can lead to things like the detrioration of soldered joints etc, quite apart from the potential condensation issues - which stem from the greater capacity of hot air to hold water than cold air, and which will still occur internally even if you throw a towel over it).
The best solution would be to work out why the computer is getting so hot and if possible doing something about it!
A CPU temp of 180ºF isn't an unusual temperature to reach when rendering video and the like, but even then it shouldn't make use of the keyboard itself uncomfortable.
Personally I'd dump the smcfancontrol software, as , in some circumstances, it seems to lead to more problems than it solves on MBPs.
How do you use the computer? On your lap? on a table? No evidence of blockage to the vents? Can you actually hear the fans running flat out when the temp is high?
What are you actually running when the temps get this high? Is it happening under OSX or are you running Windows at the time? Any sign of a "runaway process" if you take a look at "all processes" or "active processes" with Activity Monitor? (see
http://support.apple.com/kb/TS1473 for instructions).
Cheers
Rod