Once again I have to point out the extremely small size of the warhead of the stinger and the very heavily built engine and support structure of thee 747. If it did manage to avoid the ECM and automatic flares put out by the defensive system the missile would home in on the nearest heat source which is the outboard engine. There have been numerous examples over the years of a engine falling off and the plane flying on normally; more examples of a blown engine and no problems. The missile would enter either at the rear or front of the engine and its explosive force would be channels by the design of the engine to a certain degree as well.
There is a less then 5% chance of the missile hitting the plane and less then a 1% chance of it doing critical damage.
OK, but you saying it doesn't make it so. Do you have any evidence?
I don't think there's any dispute that ECM/flares would make the chance of a hit low (depending on the generation of missile used from a SA-7 having no chance to a latest model SA-18 or Stinger-B having some chance).
However, there does seem to be evidence that the loss of an engine + lift and control surfaces on one wing is a potentially fatal threat to an aircraft, even a big one, particularly just after takeoff.
This article for example claims that the SA-18 has a 25% chance of killing a target using both flares and ECM, not 1% as you state, so I'm wondering where you got that figure from?
In favour of the idea that big aircraft can survive attacks however is the outcome of the
2003 baghdad attack which didn't succeed in destroying its target.
Also, possibly a Command Line of Sight missile such as the British Javellin or a laser guided missile such as the Starstreak would be more effective than an IR homer.