It makes sense that the rebels didn't know about it. It doesn't make sense that the first the audience hears about it is that line. It feels lazy. They could have mentioned, in an offhand way, that the remnants of the Empire is pursuing cloning tech. Not only would this tie the final trilogy to the second trilogy. (First? Episodes 1-3, anyway) But it would also make that line make way more sense.
As as much as the Thrawn trilogy feels like bad fanfic, it does tie the whole clone wars/rebellion thing together, and features someone who comes back as a clone. I think it would have made a way better trilogy than what we got.