I wonder if you really wanted to go over at all? I mean if some girl asked me to come over after work, my first question would have been "great, what time?"
I think she's got a point. I wouldn't have waited two hours for you. If I had asked a female to come over after work and she wasn't around for two hours I'd be pretty angry. Just me, but you asked for the advice, so...
Your call. You want to make it up to her? Then you apologize PROFUSELY for the misunderstanding (whether you think you're wrong or not) and you don't let it happen again. Next time you say "Love to come over, what time would you like to see me?"
You don't care, then I'd blow it off and plan on not seeing her after work ever again.