Not quite, Anneke was asked to stay for longer, but didn't think it was fair on Micheal, who's wasn't renewed. It's possible they were only contracted for so many episodes, and their departure scene was shot on film so may have been shot weeks earlier anyway.
Indeed, their departure scene in episode six was shot with the rest of the location work between Macra Terror 4 & Faceless Ones 1, so their last work on the series was the studio for FO2.
And, as you suspect, their contracts for so many episodes had been issued before the number of episodes in each story later on in the season had been tied down, so they ran out in mid story. The oddity is that it wasn't halfway through Faceless One - they were both under contract and paid through to Evil of the Daleks (episode 2, I think, but I've not found the reference to check). There's been speculation that they were originally going to be left behind in 1966 London when the action in Evil jumped back to 1867 Canterbury, but the surviving story outlines, etc, don't back this up).
Their departure is a bit odfd and perfunctory, but the best explanation is just that having decided to switch to Jamie and the new girl (and that was originally going to be Samantha/Cleo/Mary, before ending up as Victoria next story) producer Innes Lloyd wanted to make the change as soon as possible.