Yes, I absolutely agree with the condenser system being too much for most any server. Removal of such an item would almost be absolutely necessary. However, (and let me know if I am wrong on this), but you can't just pump things into the transmutation tablet. And as for manually dumping quarried cobble into a tablet, I would personally rather not. (There are some people that will dump a stack of cobble for a piece of redstone over and over again, but I would personally find it really annoying.)
Infinite-generation machines are going to inherently break the system. I can see your point on that. However, a change in default EMC configured values can also lessen this issue. By doubling or tripling the values of higher-up EMC items (Make sure you keep everything scaled appropriately. You could also consider making low-value items such as cobble have no EMC value / not be transmutable, which is also a possibility.), you can scale the system to be more appropriate for multiplayer.
Again, correct me if I'm wrong, but EE2 has configuration for both banning items and default EMC values, last I checked. Despite the mod being inherently flawed as a whole (which is why EE3 was started, but it looks like it'll have some of the same inherent flaws), it can be bent to meet the needs of most people. Yes, it'll take time and patience, but honestly I see much reward in doing so, and it can make a server a more interesting environment in general.
EDIT: The EMC scale is a 2^x system. By making it a 3^x system or a 4^x system, you are inherently devaluing the lower EMC-value items and making the higher EMC-value items more valuable, due to the exponential curve. Certain scale-downs on some items may be necessary for a 4^x system, but it wouldn't take too much math to accomplish a decent system. Now, individually mapping EMC to every item will take quite a bit of time (more depending on the mods you use), but again I would find this to be a worthy cause in the long run. You might even check the community and see if someone already has a system they configured themselves, and see if they could let you use their configuration.