I wouldn't use WD-40 for anything. Its sold as such a general use lubricant, it gets "everything is a nail" syndrome. The last place to use WD-40 is in a lock, unless you want to be calling a locksmith down the road for help when the mechanism gums up for good.

I personally use on all U-locks Super Lube from Radio Shack. It comes in small squeeze bottles, and is basically teflon held in suspension by a solvent. I've found that this can work for a whole season with one application. Its not a rust inhibiter, but you are looking at surface rust on the Kryptonite locks which isn't going to cause issues. An application of this stuff in the keyway (assuming a new flat key Kryptonite), a couple drops on the bolts and the areas where it touches the shackle, then opening and locking it a few times should result in trouble free operation.

Disclaimer. I live in Texas. The weather here is pretty gentle on stuff, so stuff that works for me may not work for someone who lives in a climate where salt corrosion from sea air and road de-icer would be an issue.