Yep, wanna is fine in informal conversation. No worries there.

Grammatically, the last sentence should be part of the previous sentence, separated by a comma. This is because a clause beginning with "In which case" cannot stand on its own as a sentence. (although keeping in mind that this is meant to be spoken out loud, the punctuation doesn't matter as much – however, it's still important in order to transcribe it correctly.) And the "left us no choice" should be in the present tense because it's a consequence of something she might do. So, I'll change the last sentence to this: "Though she may wanna conduct the seminar at 2 (anyway), forcing us to attend it, in which case some might agree and leave us with no choice but to attend (as well).