The alpha pep66 on your system is one of the best ever created for that application, the absolute envy of every geek of that era. The fan should exhaust air away from the sink, rather than push air into the sink- all the old fashioned alphas worked best that way.... it's how they were designed...
I'd look elsewhere for the problem, particularly to see if the sink is clogged, correct paste application, weak spring hold down on the sink, stuff like that. Try running the system with the sidepanel off to eliminate case airflow issues. And you may just have screwy software...
If you're not overvolting the processor, overheating won't hurt it, anyway. They're tough- they just quit working, and can be restarted again once they've cooled off.... they won't fry like some more recent designs...