It depends on many things -- context, circumstance, your relationship with her, the things said at the time, all that happens before and after the kiss. Most of all, what's on her mind about it.
In the end, she judges it. It's her decision whether it's ok or not.
In that case, it's the same as it has been for centuries and millenia. You take a risk, and either she likes it and the risk pays off or she doesn't like it and you're in trouble.
In Kagami's case, she prolly screwed up. Because...
Remember how in Marimite an older girl would make a younger girl her "petite soeur" and protect her and dote on her? Well, this military school has a similar tradition: a sempai can make a kohai her "maiden" and enjoy a privileged relationship with her. And in chapters 6 and 7 we find that...
A very confused Shinobu is trying to understand why she was kissed by Kagami. She hears about the "maiden" tradition and thinks that, hey, that must be the explanation: Kagami has taken her as a maiden, and that's the reason for the display of affection! She goes to Kagami hoping to confirm it... and Kagami says NO, she doesn't want Shinobu as a maiden. But, but, but... why the kiss, then? And Kagami replies that it was because she damn felt like it -- when she wants to kiss someone, she just does it, and doesn't accept any responsibility for it. >_<