Cid in IV didnt make his airships to be used as weapons. He wanted no part of any of the bad things going on in Baron, which was why he was imprisoned.

None of the Cid's were ever doing anything maliciously. They were all doing what they thought was right, not set out to be bad guys. In VII, working for Shin Ra did not make you evil or bad. Shin Ra was bad, but not everyone who worked for it was. Especially not at the point in time when Cid was working for them.