I think that we need to make a distinction between when an airline is willing to make an accommodation (when possible) and when an airline cannot (or will not) do so.
If Continental is willing and able to give up the kitchen for the time period for a minyan, and it does not cause a Chillul HaShem, then it should be obvious that as long as there is no danger, one should daven with the minyan.
However, just because Continental is willing or able doesn’t necessarily mean that other airlines can do so as well. They may have different in-flight policies (which may or may not be easy to change) that may preclude the giving up of the kitchen (or other area) for a minyan. In such cases, where there is going to be a chillul HaShem, I think it is just as obvious (based on the comments above) that it is better to daven in your seat.
It goes without saying that if one is actually causing a danger to the aircraft or fellow passengers that you cannot daven standing up in the back of the plane.
The Wolf