I'm super ambivalent about this. On the one hand, Thaumcraft, and many other mods like it, is so deliberately NOT the "stick items in a grid, shift-click the output." The intricacy of crafting is truly a core element of the mod. On the other hand, people who install and use EE are using it BECAUSE they want to skip the crafting process. Shouldn't those people be allowed to play the way they want? It's really a quandary.
I actually think the practical effect of your decision to remove EMC values from many items will help EE become more appealing to most server/modpack players. I'm just not sure it's in the "spirit" of EE, whatever that means.