Is it a balk if third baseman is holding a runner on in foul territory while pitcher throws to the plate?

Pretty much if the pitcher does anything other than pitch the ball while his foot is on the rubber, it's a balk. He must always disengage before doing anything else.

With that rule aside, the rest of the questioned incident is balk-free. A pitcher is allowed to throw to any base, occupied or not, to stop a steal attempt.