The 1D MK III does make a pretty loud noise, I can understand that it might not be what you want in noise sensitive situations.
That is where a mirrorless camera would come in handy, particularly one with in-lens shutter instead of focal plane shutter.
If I were doing a lot of work in situations like this, I'd look for a camera that was inherently quite, rather than adding a muffler. Unfortunately, you must give up some of the other desirable features of the 1 series bodies to get mirrorless. Sony may be out with a new higher end pellix model soon, that might be worth looking at for quite situations.