Have you looked at Saris racks? They are cheaper than Thule or Yakima but seem of good quality. You don't need to buy all sorts of lock to lock on all the bits and pieces (although the bits and pieces can't be removed when the rack is locked on. There is a mechanism that lets you adjust the width while you are attaching the rack which avoids scratching your roof. I have one on a Prius which has a very short roof. I carry a 17' Guillemot, using bow and stern lines to the hitches under the corners of the car and it seems very secure.

Ric