At first I agreed with the interpretation that you could not have a spell obtained from arcane disciple be a spell-like ability, but now I'm now not so sure. It specifically says the spells granted by the domain become arcane, so that isn't the problem. The issue is the line:
"Each day, you may prepare (or cast, if you cast spells without preparation) a maximum of one of these domain spells of each level."
Relevant archmage text:
"An archmage who selects this type of high arcana can use one of her arcane spell slots (other than a slot expended to learn this or any other type of high arcana) to permanently prepare one of her arcane spells as a spell-like ability that can be used twice per day."
You're only preparing it once, and casting a spell is not the same as using a spell-like ability.
Am I clutching at straws here? Would this ever fly? Straight yes or no to this last bit please.