The slap I'm pretty sure was out of jealousy. If it had been the reason you stated, she would not have worded it that way. She would have said something along the lines of "How can you kiss me bla bla" or "I can't do this because of Setsuna bla bla."

Saying "How many times have you kissed Setsuna!?" indicates that the problem lies in "kissing Setsuna", not the current kiss, which she was happily enjoying until Haruki went all tongue master on her. Guilt would not have necessitated many kisses or even one. Guilt should exist because Haruki and Setsuna are in a relationship, (and they are cheating) regardless of how developed that is. Jealousy on the other hand, directly increases with the amount of closeness the two have, which I believe was reflected in her outburst.

I don't think Setsuna saw this coming to this detail. Of course she didn't think Haruki would cheat (and I am willing to bet the characters in the show and the audience didn't really think so either), but she had to know that the chances of their relationship going well when she knows her boyfriend and best friend are in love with each other is pretty bad. That probability simply came true in the worst form possible.

Setsuna confirmed that Touma loves Haruki (a lot) when she saw that sleeping kiss. Remember how she acted when she wanted to get permission from Touma? She acted like she was unsure of how Touma felt, and that she was convinced that they (the 3) were going to be fine when Touma said so. She did all that, knowing how deeply Touma felt, and how clumsy she is in being unable to express that. How can she even think that it is going to work out after seeing that kiss?