If the book has to be read to understand the movie, then Lucas failed. Lucas has called himself a "visual storyteller", so it's preposterous to think that he left this little nugget in for the fans who read.
"Lucas decided not to include it in ROTS, in order to focus more on Anakin's story"
Rather than being part of this carefully constructed plot to get SW fans to read EU, as you appear to imply, what it really is is something that could have been made into an important plot point, but was utlimately dropped like a fart in the wind so that we could get a few more minutes footage of a burning ship crashing into Coruscant.
You have apparently been made to be left guessing, but I, like Lucas, have dropped it as unimportant. And as for the EU explanation: a Jedi Master really initiated the order, without the Council's or Senate's knowledge, yet giving his true identity to the Kaminoans, and somehow coming up with the tremendous amount of funding to start the order, all in the hopes that the Republic would readily accept an unsanctioned army when they are not at war?
Puhleeeeeeeeez! I like the EU, but this is just flat-out ridiculous.
Then again, that does sound like a contrived scenario that Lucas would come up with......