After playing with EE in SSP, I'm pretty confident the only thing that really needs to be disabled in EE is Nova catalyst/cataclysm, especially in the nether with nether ores enabled and all.
I ended up yanking nearly a stack of nether diamonds out of there with one TNT, one mobius fuel, and two aternalis fuel, all of which were made out of coal i'd already dug up by the time I could make a philosopher's stone.
Server owners might want to limit the number of energy collectors players get due to performance issues(or at least require they make mk3 collectors/relays before making a new one), but I don't see why it'd need to be outright removed. You can't make a diamond out of 64, or even 512 cobblestone anymore. It's 8194 or something close. The progression seems to mimic buildcraft quarries more now. You dig up 11 diamonds, you make a quarry. Your quarry digs up 11 diamonds, you make another quarry. Your quarries dig up 11 more diamonds, you make another quarry. And so on, and so on.