It's highly likely the emergency contraceptive pill you took is making her bleed, and will likely cause intermittent bleeding for the next month or so - and could delay her usual period at least for one month. Additionally, if you aren't having penetrative sex, there is no way she'll get pregnant. A few sperm deposited at the outside opening of her vagina won't be able to swim all the way up to an egg, without seminal fluid to neutralize the Ph.
It sounds like she's having some hesitancy in having sex, although you're married. Has she had a check-up by an OBGYN to see if there's a problem that's causing pain?
Sorry, meant to say the pill SHE took.