Hmm... While 90% of France may be Catholic, Europe has a lot of non-practicing any religion people in it. So while 90% may identify as Catholic, not all of them may be practicing. So, maybe only 10% are actually practicing.
The other possibility is that the French Government itself is a secular government. As opposed to the Englsh Government which has the Queen as the head of the government as well as the head of the Church of England. I think this is the more likely possibility. Remember, Hellsing is still a government agency.