This:
Code:

PlayerPawn(Other).PlayerReplicationInfo.Team 

is what I needed.

Code:

Class PaintballMutator expands Mutator;
function bool CheckReplacement(Actor Other,out byte bSuperRelevant)
{
if(Other.Class==Class'DispersionPistol' || Other.Class==Class'Infiltration.INFIL_M9')
{
if(PlayerPawn(Other.Owner).PlayerReplicationInfo.Team==0 && ReplaceWith(PaintballPackage.PaintballGunRed)
return false;
if(PlayerPawn(Other.Owner).PlayerReplicationInfo.Team==1 && ReplaceWith(PaintballPackage.PaintballGunBlue)
return false;
}
return true;
} 

Try that; I made it now. It should work. Notice one thing: replace PaintballPackage with the actual package name, PaintballGunRed with the red paintball gun name and PaintballGunBlue with the blue paintball gun name.

Good luck.

P.S. Matrix, thanx for the hint.