Bavaria was an ally of France up until 1812, where it swtiched sides to join the anti-French coalition. In the game as it now stands, this would be represented in 1 of 2 ways, Bavaria could be the target of a successful coup by Austria or Austria could conquer Bavaria through the occupation of their capitol. Either way, Bavarian territory would become Austrian conquered. The next turn, Austria turns Bavaria into a protectorate and it is in the fight against the French (and forming a new army after the patch).
Oh, and as for Bavaria and Holland having "full control" over their armies, I disagree. Bavaria supplied France with troops for combat everywhere from Austria to Russia, where they were integrated into the French VI Corps. I am sure the Dutch were about the same.
Your proposal would also prevent things like one of Napoleon's hopes during the 100 Days, where he planned to defeat the Brits (and their allies including the Dutch) and Prussians and get the Dutch to switch sides (in the game, to switch from a British protectorate to a French protectorate).
Irrespective of all of this discussion, I believe the patch is essentially complete and just in testing stages now. I don't believe that anything like the restrictions on conquering protectorates that you propose are included.
Russia in "Going Again II"
France in "Quest for Glory"
Prussia in "Invitational"