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And please, don't take my post as me thinking I am right and you are wrong; I just want to get a better understanding of this all. 
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No, not at all, you have a pretty good understanding and ask good questions.
First of all, winds can vary dramatically, but 100-150 kts at cruising altitude is not uncommon at all, regardless of what they are doing on the ground. I have also seen winds calm in cruise, though that is quite unusual. Temperatures are usually in the -55C range around 40000'.
So your thought is correct at lower altitudes, that without airspeed indications you could use groundspeed to give yourself an idea of what your airspeed should be, because they will be close, with the primary difference being head or tail wind. As you go up in altitude, the difference between the indicated airspeed and the true (corrected) airspeed becomes much greater. Ex. at sea level 250 kts indicated is basically 250 true, at 40000' 250 kts indicated is well over 400 kts true (due to pressure and temperature). However the airplane still flies as though it is doing 250 kts areodynamically, hence the importance of indicated airspeed. Then add winds into the equation, and you can see how groundspeed at altitude is of no real use when dealing with aircraft control.
The more appropriate way to deal with a loss of airspeed indications, whether at low or high altitude, is by looking at airplane attitude and power setting. Basically, with the proper power set in the engines, and the appropriate airplane pitch attitude (maybe 2.5 degrees nose up for cruise, or 10 degrees for enroute climb), you should be close to the desired airspeed. In the Mayday scenario you are talking about, if they looked at their pitch and power, they would have realized that the indicated airspeed they were getting was illogical, and could've attempted to correct it. Easier said than done of course, but that is how a crew can deal with erroneous airspeed indications.
I hope that makes some sense...