Hi c_t
If the mission isn't that big you could put a little script on each radar or IR-weapon armed unit that stops them from firing if the target's ECM flag is up. Then just put an addAction on the target that sets this flag for a brief period (say 4-6 seconds) while spitting out flares or playing a sound of some sort.
For example - you could have four Strela dudes and a radar armed Shilka, all with the script "ECMCheck.sqs" running from their init fields. The target (say a stealth fighter or black ops Cessna) would have the addAction "ECM.sqs".
ECM.sqs would simply set a varaiable called ECMActive to true, play some sound or whatever, wait 4 + random 4 seconds, then set the variable to false.
ECMCheck.sqs would simply check every 0.5 second - if ECMActive was true at that time then it would setCombatMode "Blue" (never fire), otherwise setCombatMode "Red".
Note that the faster you make ECMCHeck loop the more effective the ECM will be beacuse there will always be a brief period when the shooter is clear to fire even though the ECM is active.
As the old saying goes - this is a feature, not a flaw !
Just one possible solution . . . :-\