One of the main things I would consider is where is the point of contact for retention. If you can design the sheath where it will hold at a point on the blade or bolster somewhere then you could add a few layers of tape to the wood during the molding process. Then your finished sheath will only lightly touch the wood or not touch it at all and all the pressure and any possible abrasion will be at the metal.
I'm not saying kydex will damage wood, especially if it's hard wood and perfectly smooth kydex. I just don't really know. Hopefully someone else does.
I would think you could use the decorative Spyder hole in the Mule blade to pinch together a good retention point. Don't now how you would apply extra pressure to just that spot, but if there's a way it would be something to consider.
I have made a kydex sheath for a wood handles knife. Like Antonio stated wrap the hadle in tape prior to bending the Kydex and this should add the needed buffer between the Kydex and the wood