How worn are these tires>I'm thinking that you could perhaps run a slightly smaller tire on there and get the clearance without any serious side effects. If you post your tire size I could calculate what you'd need to lose an inch in height. Only problem I could see would be some speedometer error.
The problem with roof racks is that they need perfect sealing, so refitting another rack could be tricky. Also, I don't see how one could trim a roof rack without compromising its integrity. Your idea of substituting a standard rack is sounding better and better, if it can be easily done.