Vanilla hoppers will pull items from the first slot and the last (output) slot. This means it is impossible to automate a set up efficiently as the hopper will pull the enchanted item out of the table before it can have the enchantment removed.

This is also needed, because one needs to be able to extract the first item after the disenchantment-process is finished. I agree, that makes it hard to automate it purely in vanilla, though by all means not impossible, you just have to get a bit creative with a redstone locking mechanism to lock the extracting-hopper until the process is finished.
The automatic version does produce a comparator output if you hook one up, maybe that can help.

Maybe I could make a tutorial/template for a working system?