I have had the 100-400 for 5 years and never worried about how I handle the camera with it on. I also have owned a 300 f/2.8 IS for about 3 years, which is a much bigger and heavier lens and don't worry about that either.
They both get carried just slung over my shoulder, hanging down. When I am doing a shoot with both lenses, mounted on different bodies, they are either hanging from my shoulder or sat on the floor, resting on the lens hoods (i.e. bodies up high) and I switch by just grabbing the grip and swinging it up then putting my hand on the lens for support when actually shooting.
So both lenses are frequently just hanging there with all the weight on the mount and being swung around and up by the grip with no additional support on the lens. I have never had any sign of a warped mount, all 3 of my bodies are still as tight as when I bought them (and my 20D has had 5 years of this treatment, my 5D over 3 years).
By all means use a carrier, if you want the comfort, as suggested by some above. Don't worry about it breaking / warping the mount though, these cameras are built pretty tough and take a lot of mistreatment (at least mine do anyway
).
Many people treat them with kid gloves, never let them get wet etc., and tell others that you have to do this or they will break. Looking after your gear never hurts, obviously, but they are tools built to do a job and they can do it pretty well if you let them and don't worry about them being 'fragile', because they aren't.