I suspect that Rafa was against fixing the 3Lz entry during the competitive season (probably once she started getting tagged for it). I recall a comment he made that it isn't right to change your expectations in the middle. That's not the time to be working through technical issues...
I can't confirm that in 100%. I've seen one fan (C_T_T @FSU) mentioning that earlier, but I've never seen or read an actual interview (and I'm a compulsive interviews collector

), while I have the one where Rafael mentioned that the new rule is unfair to the skaters. Whichever case it was, the fact remains that by the time the flutz rule kicked in, Mao has already been with Rafael for 2 off-seasons, while the frowning upon flutzes/lips started already during the previous Olympic season and the rumours about the upcoming rule change soon followed. As loulou said here:
http://www.fsuniverse.net/forum/showpost.php?p=3021869&postcount=34
Mao's jumping issues were already noticeable back then and other coaches and skaters took notice of the fact that they may cause Mao grief once her body matures.
I don't want to sound as if I were putting the blame on Rafael, though. At that time the concept of "textbook technique" was still pretty new, and most coaches preferred the "if it doesn't seem to be broke, don't fix it" approach - even now a lot of coaches prefer not to mess with their pupils' jumping technique as long as the 'flaw' isn't explicitly penalized by the rules. He choose his course according to his experience and the data he had at that time.
And me? Now I have the knowledge that since then the rules became even more strict, that Mao grew up a lot and her old technique became incompatible with her body and that she's determined enough to fully commit to reworking her jumps and not become disheartened halfway. But would I be able to take the risk back in 2006 if I were in position to make the decision?
Rafael's position wasn't to be envied, IMHO. At that time Mao's jumps were still fairly consistent, so if he started messing with Mao's technique and her jumps became as unsteady as they were during the past season, he would most likely be blamed for Mao's "failures". And who knows, maybe JSF would end up taking Mao away from him, as they made Shizuka switch from Callaghan to Tarasova. At least he fixed Mao's 3T, which came in handy later.
Rafael he had a point - the sudden introduction of a new rule was in a way unfair to the skaters, as most of them had the wrong technique ingrained while they were still kids. And it wasn't exactly fair to some of the coaches, who ended up "inheriting" skaters with flawed jumps. But, in the end, I don't think it could be helped. I don't think the judges could keep on overlooking the jumping flaws when the arrival of Yutube and ubiquitous slow-mo cameras made them painfully noticeable.