In real life, if a target is locked on via laser designator, flares do NOT function as a countermeasure as long as the target is being actively lasered (to guide the missile on target). This is why in BF3 it was perfect because the actual laser designator gadget/device could only designate one target at a time and required you to accurately aim on target and track its movement.
The current problem in BF6 is that the developers failed to implement this same realistic approach, instead you now have the ability to laser designate multiple targets and the 'painting' stays for a duration even if the designator looks away: this is wrong, unrealistic and most importantly, overpowered/imbalanced.
If the devs make designation work in BF3 where if the laser designator lost direct line of sight on the target and therefore the guided missile would fail to track after the target moves behind terrain/cover/building, then the game would be more fair.
TLDR: The problem is not the MR missile/flares, its the laser designator that is too powerful since it can 'fire and forget' to paint targets and then look away (target stays painted for long duration after looking away).