The heroes' goal wasn't to straight-up murder any Shinra employees they came across... sure, Hojo was an awful person, but as far as the team knew he wasn't actually a real threat in and of himself - just a slightly crazy old man with a flair for life sciences.

Cloud and co. would've had a tough time convincing the Costa del Sol authorities that they were right to slaughter an old man in cold blood simply because "he totally had it coming" or "you should've seen what he did back at Shinra HQ."