Oh, I don't agree about shooting Hojo. Way too quick and simple.
Given my 'druthers, I'd probably go with the Mikado's suggestion of "something lingering, with boiling oil". Or maybe just popping him in a room with Sephiroth and a couple of dozen Restore materia. Or just take him to the roof of the Shinra tower and throw him off, then get someone to revive him when he hits the ground. Lather, rinse, repeat until therapy is complete.
No, I'm not too fond of Hojo. I tend to blame him pretty thoroughly for the whole slew of FFVII canon disasters, mindfucks, and catastrophes (although I will absolve him of getting Jenova to land on the planet in the first place... that one he couldn't have influenced).