I think the EMC values come from Not Enough Items, the thing that shows you the item list with recipes, and not from EE itself. You should be able to disable it in the NEI options menu.
Double-check that you can't use EE items if you're unsure that you've disabled the mod. I don't know if removing the mod file is the right way to do it, you can disable the items by opening "mod_EE" in notepad (located in your main server folder because EE is a hipster like that), scrolling all the way down and replacing the 1:s with 0:es (those that say "allowchests, allowpedestals etc.)