I really like the substitute/Mercenary idea. Splatoon eliminates team imbalance for their weekend Splatfest matches, where players choose a side to gain points for. In the event that the game is unable to fill in an opponent's side with those who signed up under that side, they fill in that team with those on YOUR side. But it's still one team versus the other.

Just give the teams the same colors that already exist so when someone calls out "push Adders" they mean "push yellow" and don't have to know that entire team is made up of Flames players. (This is in the hypothetical situation where there is an overabundance of Flames in the queue but hardly any Adders. It would never pair individuals from opposing GCs into the same team; it's an all-or-nothing contingency.)