It would actually be handled by the the C2ISTAR module. Under the auto task OPF, go ahead and set everything as you normally would. Define the opfor faction in the mission, and also define it's enemies. You would then take the exact information and copy paste it under the Auto Task IND section, however you would leave the "Auto task IND faction" as "IND". This would ensure that even when you are technically on the resistance side (JND), you are given the same tasks as you would if you were an opfor in that mission.
If I was going to setup a mission in of this type, this is what I would do. You could have the Opfor side faction be insurgents and set to asymmetric, they will then carry out attacks on blufor while blufor is busy retaliating. You would be fighting for the opfor side but due to the script, you would be changed to the resistance side which will keep you incognito (IND is neutral unless changed in the mission) until you decide to start engaging blufor. Once you engage blufor forces or take a hostile appearance (strap yourself with a bomb, pull a gun out), you will be switched to the opfor (insurgent) side and then be promptly engaged.
Terrible at explanations but hopefully that clarifies it, let me know if it doesn't. If not I could also toss you a quick mission showing kind of how you would start to set it up.