Most likely, but I don't think the factories will be wiped out unless they're moved. The Kaminoans seem pretty peaceful, but they sound like they're being used, like everyone else Palpy's come in contact with: Padme (Vote of No Confidence), Clonetroopers (galactic domination), Anakin (Vader), the Kaminoans (Sydo-Dyas=Sidious=Palpy=Big Fat Liar), and the Jedi (I want all of these clones wiped out by tomorrow. If you don't, my new best friend Vader will kick your ass).
i dont think well see any cloning facilities liked out. i think once the jedi realize what palpatines up to, mace will get the jedi their own clones. the original clones were supposed to be made for the jedi anyways, so i dont see that as being a stretch. green armored clones (bobas uniform) vs. the clonetroopers we see in EPII. they wipe eachother out and the senate passes some vote saying no more clones.