Looking around a bit I have noticed that at least tekkit servers should have a setting for how many chunks each player is allowed to have loaded at any one time. I assume this would exist for FTB servers as well (it's probably a part of Forge). By default it should be 81, but if you sat this to 4 (which is what I think a default sized quarry will use at most) you could enforce these rules.
And to continue with the discussion of chunks; an inexperienced player that follows the rules can still create quite a problem with his/hers quarry. And here is why:
If the system that handles the output (the pipes and chests and what have you) is placed in a chunk adjacent to the quarry, BUT NOT LOADED BY IT, then I assume whatever the quarry mines will be spit out where the output pipe traverses the chunk boundary. This is not easily solved by rules, one have to have knowledge about how the chunks work.
Actually, thinking about it, I think this can be one of our bigger problems. I happen to have my quarry set up so the unloading system is loaded together with the quarry, but I don't think many others on this server has taken that into consideration. This is why buildcraft pipes works so bad for servers. Check the third reply in this thread: http://forums.technicpack.net/thread...ft-hate.20665/
I hope I don't appear as difficult, it's not my intention, I just want to put forth that the solution is probably more complicated than just limiting peoples amount of quarries. At some stage chunk loading has to be taken into consideration.