Ikkajo has more the connotation of first control nikajo second control etc etc.
I would question this postulation that the original use of ヶ条 (kajou) in aikido meant for that term to carry the meaning of "control." I doubt many (if any) native Japanese speakers (outside of those in aikido) would ever translate ヶ条 as "control." Even within the context of the lineage of aikido, the original use of the term came from the Daito Ryu system of classifying techniques into sets (eg 30 techniques in ikkajou, 30 techniques in nikajou, etc). (An interesting side question might be why ippondori was chosen to be ikkyou out of the 30 Daito Ryu ikkajou techniques, and so on (nikyou, etc)?) Most likely, the use of "control" came about in offering a suitable enough translation of the term (rather than just calling it "first technique"), kind of like how some people "translate" the term "aikido" as "the art of harmony."
Likewise, I think the speculation that 教 in ikkyou (一教) carries religious connotations is linguistically/semantically off. Also, although the term 教師 (kyoushi) is sometimes used to describe those in the religious realms, to link that to religious connotations in 教士 (kyoushi) or 一教 is a stretch for me. As Chris Li has often said, just because the term "martial" comes from "Mars," the name of the Roman god of war, that doesn't mean that everyone practicing martial arts is meant to be a devotee of that god. Also, just because I may call my dad "father" doesn't mean he's a Father (ie pastor).
In my mind, the term kyou (as in ikkyou, nikyou) points to the principles underlying the techniques themselves. Each of these techniques carry a more descriptive name (eg ikkyou = ude osae, nikyou = kote mawashi, sankyou = kote hineri, yonkyou = tekubi osae) as well. Using the kyou names, to me then, points toward the principles underlying each of these techniques as exemplified by the techniques themselves. (Which principles they're pointing towards is left as an exercise to the reader, as I don't trust my experience enough to try to explain them myself. Heh.)
As far as the questions towards whether Kisshomaru Ueshiba changed the names, I'll see if I can scan some of the books he's written in Japanese and report back if I find anything. The secondhand information gathered from those during that time seems to indicate such as Mark points out above.
Back to lurking,