The pill is effective if taken at approximately the same time each day. As long as she takes it within a few hours of the same time everyday she's fine. Yes, a few hours - so like, 3 hours.
You're totally fine, and there's no reason you need to be pulling out. Birth control is extremely effective in preventing pregnancy. Condoms aren't needed, but they're a good idea to prevent spreading sti's. The pull out method does nothing - don't bother - just enjoy sex.
For the record, I've been on the pill for 10 years. No pregnancy scares. I always take my pill at bedtime. Sometimes that's 10pm, sometimes it's 2am. I have always been in monogamous relationships and would get full sti panel testing after each relationship was over so I would know I was okay for the next one. I basically never used condoms, and have never once used the pull out "method" (it just seems mean!).
Basically I'm saying that the pill is extremely effective and can be trusted as the only method of birth control - I don't know why people don't seem to trust it!!