I'm with Penny - we're apt to forget just how different life was before reliable contraception was available. If you think that pregnancy followed sex pretty much as night followed day, and that having a child meant the end of a life of your own, then let no man steal your thyme isn't so much a metaphor as an obvious pun (particularly in the versions where the 'thyme' is replaced by 'rue').

And a pox on your pox sores - I think the rose that never shall decay is sexuality, no more & no less. My reading is that, as a virgin, she didn't care about sex & had all the thyme in the world; now she does & is bound to get pregnant, sooner or later - her thyme is running out.