WHBM
Agree with much f what you say, however it falls down here:
They had no issue in France (given the French did not intercept them)
It is not unknown for French ATC to bandbox sectors and lose aircraft on frequency in doing so. It is also not unknown for them not to give a fig about a lost comms aircraft if its observed track is taking it away from French airspace. It is also not unknown for them not to mention any of this to UK ATC who are then faced with a situation with less intelligence data than they could have even though, as you say, it was a regular flight following its filed route.
Overkill by the military? Most definitely, but then again what else can they do given the history of 9/11 and the profile of the flights that were hijacked then?