Only code like this should be possible:
//initPlayerLocal.sqf
{
if (_x in (allVariables missionNamespace)) then {
profileNamespace setVariable [_x,nil];
};
} count (allVariables profileNamespace);
saveProfileNamespace;
^ Something like that has to be built into the profileNamespace function. So only variables in missionNamespace can be manipulated in the clients profileNamespace.
Prior to introduction of the allVariables function, this was not an issue.