To be honest I prefer my space to be messy to.. try and think of it like this (since I've had to explain this to many people) Perhaps he considers his house his space, and just like you prefer to have your space clean, he prefers his space do be messy, he feels more comfortable being in mess. If you have trouble reminding yourself of this just remember that his house is his space and he can have it the way HE likes it.. rather than have it the way others may like it. So in the long run, yeah it is disrespectful to go ahead and clean his house without his permission simply because clean isn't the way he likes to live. My boyfriend tried cleaning my house like you did and when I came home.. I was anything but impressed, but after I calmed down I talked to him and explained how my house is my space and clean isn't how I like it, though I try and make sure that none of the mess is anything that will rot.. After I explained this he was far more understanding and feels free to leave anything anywhere.. since I seem to remember where everything is.. I tend to lose things in a clean house rather than a messy one.
Sorry if I confused you