I had the very same problem on my tekkit server:
If you use EE just hook up an energy condensor with a piece of Red Matter as the target –I have all my materials go through an item sorting system using red power (3 sorters for very specific filtering) - I have cobble/dirt/sand/marble/gravel go into a chest which has no free slots so once each stack is full - the overflow ends up following the Pneumatic Tubes to a condensor.
if you do manage to have a huge item spill and your server gets choked up, you can use worldedit to clear the drops:
/remove drops -1
this will remove any dropped "loose" items in your world: you won't be able to get em back so prepare to lose lots of items ( I had 11,000+ drops killing my system at one point)
Hope that helps