Actually, "ai" is kunyomi. The onyomi of that character is "go". The compound "aiki" is a mixture of onyomi and kunyomi - if it was read entirely as onyomi it would be "goki". It's rare to have a word mix the two, but it does happen.
My guess is that whoever coined the term "aiki" was actually trying to distance themselves from the classical Chinese meaning of the compound "he qi", which originally referred to a Tianshi Daoist sexual rite from probably the 2nd or 3rd century AD. The term originally meant "the uniting of the qi". The qi involved being that of the two people, and knowing the Daoists, probably the qi of various constellations, stars and other things.
So, why not the tantric union of two peple in the context of martial relations as they ascend in conciousness toward the realization of their own 'stellar' divinity?( as modeled by the universe). A martial 'roll in the hay', if you will.
By the way, in the discussion 'the meaning of doka' I put forth a related and poetic response to the question 'what do you mean by doka?'. I use it to mean we are 'songs of the way' or 'poems of the way'. Just thought I'd mention it here rather than posting again. Thanks.
"I know not why, but martial men ( and women) are given to love."
Sir Francis Bacon