In a recent interview, Zack Snyder said that an early idea to introduce Batman was to show him in his cave with some Kryptonite in an end credits sequence. Obviously, he was talking about an early concept and it doesn't necessarily confirm the existence of Kyrptonite in BvS, but it does show he's not averse to using it.
Personally, I think it's necessary. There's absolutely no way Batman could physically contend with Superman without him being weakened significantly. Plus, it puts Supes in a situation where he's out of his element: he's forced to overcome a situation without being able to rely on the use of his (full) God-like powers.
Ultimately, I bet we'll see something similar to TDKR, where Bats will use everything he's got to distract, confuse, and weaken Superman, including the green rock. And I think that could be awesome.