The definitive answer is: It depends.
What kind of commercial aircraft are we talking about? A hit on an MD80 or RJ is going to be different than a hit on a 4 engine aircraft or business jet. How alert (or fatigued) is the crew? How bad is the damage? What was the weapon system? What aspect was the missile fired and where was it in relation to the aircraft when it detonated. An IR seeking man portable SAM does not always fly right up the exhaust and detonate inside the tailcone.
As for TWA 800 there are some theorists out there who don't beleive the results of the accident investigation, but I would venture the majority of experts in the field discount the MANPADS hypothesis.
Flares are not the only defence against IR threats, however your comment about defences being expensive is correct. I hope specific details regarding the capabilities of these defensive systems is not forthcoming on this forum.
This fact is certain though - The possibillity of catastrophy is close at hand whenever these weapons are fired at any aircraft.