Splinter is NOT being controlled by the Rat King.
However, Splinter is being influenced by his SON. Remember how Donatello was the Turtle who wanted to temporally ally with the personal vendetta-driven nemesis (Shredder) to oppose the global alien threat (Krang), even though the personal nemesis had already brainwashed a fellow Turtle (Leonardo)?
Splinter is doing the same thing, except he doesn't realize that the Triceratons aren't evil and Bishop IS. Splinter, you have very poor judgment.