So the 2 neutrals get into contact with each other and then what? They can still only decide to aid pro-town or mafia. Or both, but they can never win as neutral. They can only win as part of one or the other.
If the sniper does work with mafia and then decides to "go rouge", that means he's just helping pro-town, not declaring his own faction and winning like that. In the end, if he kills all the mafians, pro-town will win and the sniper will win as part of pro-town. It doesn't matter if he's declared himself lord of timbucktu, his actions have clearly made him a member of pro-town and he'll be treated as such.
Now if we do have a situation where all official mafians and pro-towns are dead, that would mean the neutral would've killed the last of either groups off. Depending on the alignment of who he killed, that would make it a victory for either side.
If it's him and a mafian and he kills him, pro-town wins.
If it's him and a pro-town and he kills him, mafian wins.