A vagina saint is the English adaptation of the Latin _vagina sancta_, or "holy sheath," which supposedly contains the _spatha Dei_ or "sword of God."
Does that seem confusing? Well, the word "vagina" didn't mean anything in English for a long time, but in Latin it's meant sword-sheath for centuries. "Vagina saint" was first used in English as a sort of awkward mistranslation by an Elizabethan, Sir Thomas Coke. He was an early dissenter with serious Puritan leanings, and Shakespeare supposedly mocked him in one of his portrayals of Puritanical types in Measure for Measure.
The term "vagina saint" was last used by Prince Rupert of the Rhine, who was well-known as an English Civil War cavalry commander, when he was discussing the proper method for conveying the royal regalia swords to France while fleeing the wreck of the monarchy. At around the same time (the mid-17th century), physicians began using the term vagina to mean the female reproductive passage, but of course both terms derive from the Latin for sword-sheath.