A likely origin of the word could be latin condere that means to hide/to keep safe. I've found two references pointing to that, it all gets back to that commercial site. Not a scientific source but sounds likely so I'm risking an answer.
I'll sum up briefly one short passage of this long article. A craftsman from Utrecht decided to make those little devices out of mutton intestine because of venereal deceases spreading quickly among the diplomats during the Congress of Utrecht that lasted several months. The British diplomats brought back several of those little devices with them. They started being made on a large scale and the name condom (from latin condere) given to them.
Maybe the question could be brought to history.stackexchangehistory.stackexchange ?
