-- Last Updated: Sep-26-12 10:26 PM EST --
Of course a "real" rack is the way to go, but this should be fine, especially if you go the extra mile and use more than the bare minimum of tie downs. With additional tie-downs, position them to be both individually effective and also so that they compliment each other. Many people carry canoes this way, and since the effect of wind, especially cross winds, is many times stronger on canoes than kayaks, this should be much safer with a kayak than a canoe. Also, many people carry kayaks on two foam blocks in a manner that can't help but be much less stable than what you propose. I'm sure you'll be fine.
You asked this question at the right time though, since someone just asked how to improve their no-rack method for carrying a canoe. Among the advice they got, you can apply all the same principles to tying down your kayak, though it will take a bit more ingenuity if you wish to establish tie-down points on the boat that are inboard of the ends (that's easy with canoes because of the thwarts, but if you are good with rope, you can create a secure harness for this purpose at any location on the hull of your kayak, and if not, I can explain a method I've used myself).