Couldn't you have shotgun/fist only for Heavy and melee only Spy?
Well I was looking at this this way, shotgun Heavy makes Shotgun Soldier useless because it's a bit of a trade off, be slightly slower but you get 100 more hp and it's a close range weapon anyways so you'd be just as effective as the soldier but move into battle slightly slower. It's also why I said that Pyro was disabled, I pretty much thought of it as each having their own completely different playstyle.
Now with the spy I think it'd depend, because I think if he got a watch things might be a tad unbalanced there, if he only had his primary and his cloak I think that'd be fair game, it's the fact that he also can't use a melee that it'd be again, unbalanced, because if he ran out of ammo it would be a problem.
So pretty much to me, he'd need Primary + Cloak + Melee, but no backstabs. If it was ONLY his melee then anyone who's spy would end up just camping a corner and it'd be near impossible to get a backstab anyways.
Edit: I'm trying to avoid instakills all together.