She might have. She got mad that Misuzu had briefly dated Jun in middle school saying, "You know how I feel about him." The only thing is, Tomo just didn't reveal that to anyone, only telling Misuzu right before they graduated. So it's possible she didn't when they first entered middle school, but considering that she got angry at Misuzu, I think she did like him.
It would have lessened the blow to hear the rest. Only listening to the first part probably hurt his confidence.
That's not a fact though. All that the conversation tells us is that Tomo thinks that Jun doesn't like her in that way, not that Tomo doesn't like him.
No even if he stayed to the end it doesn't change the fact Tomo didn't see him as a crush then.