MLAA is supposed to be better then SAA. I always found it dumb in the old AC games that SAA gave a certain kill as long as you maintained a lock on, while MLAA often missed every single target even when you maintained lock all the way in. The MLAAs are modelled after AIM-120/R-77 missiles while SAAs are modelled after AIM-7/R-27, so logically they should be an upgrade over SAA's that is available to the player later on. And realistically the MLAA's accuracy should depend on how long you maintain lock before turning away, but I'm not sure how viable that would be gameplay wise.
Yeah, its a tough situation.
Balancing them will make SAA much better weapons than it was IRL. But making the weapons realistic means that there isn't a reason to take SAA. Maybe Adjust ammo so that there are more SAA ammo than MLAA?
Not sure if that'll make a difference but for me at least I'll use it more since right now ammo conservation is more important with SAA.