Thats happened twice to my girlfriend and I. I finally convinced her to go on the pill because it is much safer than just condoms. There really is nothing you can do, depending on how long its been since conception you may be able to get her a morning after pill. Under 72 hours since and the morning after pill is a good choice.

Where was she in her cycle? (How close to her next period), because if you know that you can have a rough estimate of when she'd be ovulating?

Just take it easy man (I know, easier said than done) and I'd suggest that if this boils over you immediately talk her into taking the pill. It is the safest option if your going to be having sex, 100% effective if used correctly. It'll make her feel like shit for a while but eventually she'll get used to them and its for her own good as well as yours.