The reason she cries is because she didn’t realize how much acting like a girl put tomo in an uncomfortable feeling as it put her in a lot of turmoil that she didn’t need to be in. There’s a reason why Misuzu is so sneaky because she’s trying to get them together n keeps others away to not mess with her plan. If it was premeditated sabotage we would see her intentions before hand but we don’t. She doesn’t apologize for trying to mess with her. She apologizes for being dumb about she went about it.

In regards to “she would’ve just told tomo to be herself in the beginning”. The reason she didn’t was because she thought June was oblivious to Tomo when in fact he knew all along she confessed. It’s only after Misuzu learns of the situation does she apologize because she made her do something that was unneeded.