It's not an alliance, Tim.
It's a Non-Aggression Pact. They're simply not the same thing. Technically speaking, you shouldn't even be able to place units in other players' cities, nor vector to them, if all you have is a NAP.
A Non-Aggression Pact is a formal agreement in which two military powers decide not to engage one another, for mutual benefit. It's neutrality, not alliance.
War ----- Neutrality ----- Alliance
--------------NAP--------------------
In the end, you have to fight. It's still a "free-for-all" and there is only one winner. If you want to play a team game, then you're free to do so
If your concern is rather that NAP is a cost-free solution for players looking to take advantage of others in a free-for-all game, then that's another matter. Perhaps there should be an option for "Enforced Free for All" and then the typical game where players may make what pacts they will?