Perhaps she was trying to physically remove him too. The article is so short and doesn't give many specifics about the case in question except for the recent decision of the justices.....so, I'm afraid for some things we will all be giving 'the benefit of the doubt' to one person or another - the guy or the girl.
If the girl was trying physically to stop the boy's actions and he overrode her efforts, that would be grounds for a rape charge whether or not she said anything; were that the case, though, it would almost certainly have been mentioned.
Also, I just have a really hard time with the notion that a girl who was being raped would say "I need to go home". It sounds much more like something that might be said by a girl who was having second thoughts about whether she should be having sex, but that is very different. Further, in most other contexts, a statement like "I need to go home" means "I'm in an extreme hurry; wrap things up quickly." And I don't doubt the guy was trying to do precisely that (though I'll admit I find it a bit odd that a 17-year-old would take 90 seconds... thought they were faster than that).