The reason that java is wrapped in .net is because java hasoffers the concept of build once, run anywhere. So it makes sense to base it on java, and for .net implementation simply wrap it instead of rewriting the whole thingAPI.
As far as .net shops who aren't comfortable with java modules, it's a moot concern because SDL fully supports this fuctionality and these .net shops do not need to deal with whatever java is deep under the hood.