Not hurt her, no. They were trying to take her back to Shinra HQ.

[Because she was the last remaining Ancient. Once again, he didn't know how much Zack knew about Aerith's past, but he'll err on the side of caution for this one. It wasn't as if it was his secret to tell anyway.]

They eventually got to her in exchange for a little girl's safety. But we made sure they didn't have her for too long.

[He, Tifa, and Barret owed it to her to get her out of there, after all. So he made sure to at least reassure Zack of that. In fact, he might be looking a little proud of himself for that.]