The SA-7, HN-5, and the various Ayn as Saqr variants only have 2.5 pounds of high explosive. They seek out tailpipes.
One quick field response would be to weld longer exhausts down and away from one side of each helicopter. 10 feet away from the engine/fuel tank/cockpit would make a world of difference against 2.5 pounds of HE.
The launchers for those missiles have passive radio frequency receivers that point the operator toward an aircraft that is transmiting radio, has a Mode-3 or later transponder, or has an active radar. May have to turn those off for a while, boys.
Also, keep in mind that Al Qaeda was working on a chain-based ground system in Iraq to take out helicopters, plus Iran is fielding air-burst proximity-fused RPG's.
Owning the skies doesn't mean that you own the dust-zones. Helicopters are vulnerable to these new threats. Just as cavalry adapted in the past, obseleting old horses and embracing new modes of transportation, so too may we have to do it again (and expect similar levels of b!tc#ing from the horse lovers).
FYI, passive radio frequency receivers were what Hezbollah used last year to roughly track the location/direction of Israel's tanks in Lebanon...
So passive radio frequency receivers aren't just being used against our helicopters in Iraq.