It in fact originates from the constant warfare between England and France many years ago, at that time "French" was associated with indecent things and activies (Swearing, kissing etc).
What the English might call the French disease, the Dutch might call the Spanish disease, the French might call the English disease and so on.
"Pardon my French, but Cameron is so tight that if you stuck a lump of coal up his ass, in two weeks you would have a diamond." or "Pardon my French, but you're an asshole!"
Guy 2: Sometimes you gotta go with the flow and just stick it up the poop shute.
Guy 1: Ya, i know what you mean. I hope that she can Pardon My French.