Why, "please misinterpret it," though? That's such a weird sentence. It's like asking not to understand your intentions. I know I should be focusing on the Yuri but this is distracting.
Tomoe is expressing that she "misinterpreted" the draft as a confession. It actually wasn't meant to be, and the author starts to try and pedal away from that with excuses because she doesn't think she'd be interested, but then Tomoe is visibly disappointed. So she asks her to keep her misinterpretation and take it as a confession.
I guess that's the conversational equivalent of a double negative - and as easily confusing, it seems.
In that sense, her rebuttal was not nonsensical...