We can't assume that the NuTrek cast will have the same longevity after the 3 movie deal is done, particularly when Pine and Saldana's stars are on the rise.
Which doesn't mean anyone's going to be written out in the second
Still, I suppose that now they've bitten the bullet once, they could always re-cast characters as and when required if they want to carry on beyond the third movie.
Just what I was about to suggest. These are already the second set of actors to play these characters, so more recasting is always a possibility. And other film franchises have managed to get away with recasting characters -- James Bond being the classic example.