Either of these locations sounds good really. The main thing is to not be disturbed.
As for Shinji's reason to accuse Hermione, she pissed off Shinji too much at this point. Basically cutting to the quick with the comment about being thrown away. Natsumi already knows Shinji and Hermione met, and that they are not on the best terms, having witnessed that in the Raven common room before. Don't necessarily want to worry Natsumi about his memories being messed up, as she could very well attack Hermione in revenge. (Thinking she used the obliviate spell on him or caused a concussion)
Different story when Natsumi is aware of Shinji's missing memories' episodes later.
Could go with a write in like yours Skull, only without the memories blank. Something like [ ] Shinji and Hermione had an argument.
It's enough to satisfy Natsumi's curiosity, as she wouldn't expect another result. The puddle is just whatever.