CPU at 100% for a long time - Harmful or not?
Solution 1:
100% CPU utilization will not directly be harmful to your laptop. Heat, however, can be. Your MacBook Pro does have several internal temperature sensors that will turn on the internal fan and finally halt the machine should it get too hot. You can see the temperature each sensor is reading by using this free program:
http://www.bresink.com/osx/TemperatureMonitor.html
You should still use some type of cooling stand if possible. My 2007 MacBook Pro suffered a broken display from what I believe to be a heat related issue. After heavy use and high CPU utilization the bottom of the display would get very hot. Then, the screen would start to flicker slightly (but only when the laptop was running hot). Eventually, the screen had to be replaced. Using a laptop stand with multiple fans kept my machine running cool enough to prevent the issue from happening again.
Also, you do have some control over how much CPU a process gets. For that you can use BeNicer, another free piece of software:
http://frozenheads.com/page/benicer
Solution 2:
i would assume that 100% usage doesn't really mean that it's at it's full capacity and about to explode, but more that the CPU is does as much as it has been limited to do at one time, so it's kinda already capped.
The concept of overclocking is to push a computer to it's absolute limits and squeezing out as much "power" as possible, which has more chance of causing issues with overheating that could potentially cause damage.
As you said the CPU should be designed to be used upto 100% and shouldn't cause itself serious harm and as SomeOtherGuy said, it should protect itself from damage should it start to overheat.
Incidentally, my MBP gets ridiculously hot from being sat on charge all day, so I have resorted to having an external keyboard to stop my palms sweating while typing. The computer itself hasn't been affected by this obviously - any slow down is more likely to do with how much guff is on it and that I don't really maintain my computer. It'll be getting a reformat soon to clean it up and back to full speed.