OP - use the restroom changing table or ask the attendants for their opinions on what to do if your plane does not have a changing table and bring some disposable changing pads with you to put on the changing table.
I couldn't agree with you more! Our DD had BM's on both flights last Fall and I changed her in the plane's restroom and I plan to do so again in a few weeks when we fly if she has BM's during the flights, even though she is tall for her age and will most likely be cramped and uncomfy for a few minutes. I'd rather deal with that than risk possibly making someone else sick from any feces that may get on the seat.
I know how tight those lavatories can be, especially trying to change an older or larger child.
I guess I just don't want to see anyone getting sick (especially a person who is immune deficient) from the actions taken by a previous person on a prior flight.
). I also did not think the bathrooms were big enough for a changing table. I am also sure I will need to change at least one of my kids while on the plane (they will be 7 months and 21 months) because my oldest usually poops a couple times in the morning and our flight is early in the morning. Fortunately for me my DH will probably do it because he always does it in public bathrooms cause I hate trying to hold everything and manuever everything since there never seems to be a clean place to put stuff down. Yeah I have an awesome DH! 
Don't worry though...if all else fails, ask the flight attendants for their opinion on the best place to change a quick diaper. 