It would be interesting to know to what extent did the existence of a legal foundation actually constrained Morihei Ueshiba. It would be difficult to argue that the founder "became disenchanted with the transformation" if in practice he was free to continue to do with his art as he pleases.
In addition, 1942 was a turning point in the war in the Pacific (Midway , Guadalcanal). Given the strong connections with the military, Ueshiba may have been privy to this information and form an educated guess as to where things were heading, so another interpretation may be that he was just getting out of harm's way.
I do not think it was the mere existence of the legal foundation that constrained Ueshiba, so much as the presence of the Dai Nippon Bukokukai lying behind the legal foundation. In 1942 this organization was reorganized and included aikido for the first time. Stanley Pranin did an interview with a man named Hirai, who appears to have dealt with the naming, but there was far more background to the giving of the name than was suggested in Stan's interview.