Another option if you don't like the prevalence of MANPADS is to use the Mobhack tool that is provided with the game to edit the radio codes. Set the last digit to 1 means that AI will tend to skip the unit during purchase. This isn't a guaranteed cure, as the help file says:
"
Rarity" in game terms does
NOT necessarily mean "Rare". When the AI picks units for it's formations it starts at the bottom of the list and works up and it tends to favour the first thing it finds.
Try it, might make a difference. Andy and Don have been very good to us fussy gamers with lots of ways to adjust gameplay to suit personal tastes

. How many other games can you think of that are so flexible? Not many I'll bet.
Personally I'd like to see aircraft allowed in the core but I respect the decision not to do this and it doesn't stop me playing (to obsession

). There is enough scope to modify the game to suit almost every preference, so try out a few different options.
If the radio code thing doesn't work there is always the option to make some very radical changes, like giving each MANPAD unit only 1 missile, or chopping the units completely. That would make a very big difference and in my view is a step too close to cheating, but it can be done.
Health warning - any changes you make are entirely at your own risk, and don't use a modified OOB in PBEM. Scenarios and campaigns could be seriously wrecked as well.
I'm just pointing out that these options are possible - the choice is yours. It's a game and we can all enjoy it in the way that we like best, there isn't really a right or wrong here.
cheers,
Tim