If there had been more fishing ships, and/or those fishermen had been stupid and armed themselves, then fired on Canadian vessels, there probably could have been an actual war. But it would take a friggin' lot more ships, just saying.
EDIT: Actually, now that I think about it, if you could have had the International Court take up the case in '95, and rule in favor of the EU, then have Canada continue to capture fishing ships in their waters, you certainly could have EU sanctions on Canada and a significant deterioration in relations.
EDIT 2: Or, if you had the French keep the Newlyn impounded, we might see a permanent break between Britain, their little terrier Ireland, and the EU. But definitely not a war, here.