As someone who used to fly very regualrly into RAF bases as a civ flight.
It really doesn't matter a toss.
QFE/QNH all RAF pilots can operate on QNH and all civi pilots can operate on QFE its not a bloody problem.
If it means that the boy's in theater can get even 1 minute extra on the phone or one of the most piddly little bits of kit which makes life more comfy don't change a bloody thing.
The very small amount of ball ache involved is worth it compared to spending a sodding fortune changing everything.
I do wonder how many of the civi pilots with very strong views on the subject have had to operate day in and day out using the system. It really doesn't matter.