I think the reason the IIA is disabled on most servers is that the 109E's FM is off in terms of top speed, so until the FMs are corrected in a patch people are trying to balance things out on their own.
This is not only a 109 issue, in fact after tests done by the community members (the results are in this forum) the Spit IIa is the only aircraft that is getting its real-world performance in the sim.
Most of the other fighters, both axis and allied, are slower than they were in reality so the Spit.IIa becomes an "i-win" choice. I'm sure that when all the other fighters are tuned to better reflect their historical performance (auto-mixture fixed, 109s getting their correct speed, 110s getting the improved engines they used during the BoB, Spit Is and Hurris getting the 100 octane boost limits) the Spit IIa will make a return.
Until then, it's not only too much to handle for the people flying 109s, it's also too unfair to compete with for kills for the people flying other RAF fighters-->everyone on the red team would fly an Mk.II and things would be boring without Hurricanes
