the brakes themselves will not be compatible with mtb levers, but as long as you are running the same size rotors on both bikes front/front and rear/rear you will be fine. brakes themselves don't care about what they are squeezing, as long as its there in the right diameter.

i have only test ridden the la cruz, but id be tempted to go with a 180mm rotor up front and 160 out back, for ease of interchangability for the 29er. my friend overheated his 160's quite regularly on long decents, and switched to 180s for better fade resistence and more power.