I've been struggling with altar automation too. How did you end up stalling AE2 to only input one rune at a time?
The ME interface is set to only push items when the target inventory (the chest on the right) is empty. The enderIO conduit is set to only pull items when the alter has no redstone signal and has living rock blacklisted. It outputs to an aa (I'm using 2, one for the wand, and one for items, but 1 would probably work). The ExtraUtilities node has a hyper filter and 64 living rock in it's buffer, and is set to only pull living rock when the alter signal is 1 (xor'd with the 2 signal so it's only on when the alter is powering up). The conduit on the left chest (the one holding the living rock) moves the living rock to the open crate when the alter signal is 2.