There are apparently a bunch of different meanings for it and noone knows what the original one meaning was for certain according to wikipedia, but the "official" one at the moment is as follows...
"Also known as a “reactor trip,” “scram” is actually an acronym for “safety control rod axe man,” the worker assigned to insert the emergency rod on the first reactor (the Chicago Pile) in the United States."
Here is the link for reference, check the Etymology section for a breakdown of the different possibilities.
Scram - Wikipedia, the free encyclopedia