I'd have them destroyed. They didn't add anything to the game that was necessary as far as I saw. Sure, the main story started off focusing on them but after you leave Midgar, it's all the hunt for Sephiroth. Shinra becomes no more important than the side stories iN Corel, Cosmo Canyon, etc..

I'm not saying we shouldn't have multiple antagonists or anything. To the contrary, I think FFVII desperately needed more Hojo screentime. He was a good villain and could have done a lot more if he hadn't been bagged down with the useless other Shinra employees.