It is unexpected, even if Stiles has said something has been building between Scott and Isaac, Allison hasn't been around to witness that. He doesn't push Allison to talk, as uncomfortable as the silence is. He just waits until she's ready to ask any questions she might have...

Like whether it's romantic or not. It's a resounding yes, but Scott nods at her.

"I didn't want you to find out from someone else or by accident..." Especially with Allison living in the same sector as Isaac, she might have seen Scott coming out of Isaac's suite at some point, maybe even caught them kissing. Telling her himself seemed more... respectful.