I can't help you with the kitchen / butchery problem, but I have a solution for the crematorium.
I usually make two stockpiles for refuse - on in the open where things can rot (right besides the crematorium) and one insides, near the craftsdwarves, leatherworkers and all that. Select as settings for the outside stockpile corpses and refuse, but limit the refuse to: Corpses, body parts and all item types except fresh raw hide. Now, only things you don't need for anything important will land there, and by setting the stockpile to give to the crematorium, you can assure that it only takes from there.
All your bones, raw hides, wool, skulls, ivory and the like will be safe.
Drawback: On this stockpile will also be stored the corpses of your own dwarves until they get buried. To avoid, turn off the corpse setting (not the refuse - corpse one) and put them somewhere else.
If you are using the crematorium all the time, you might lose a few corpses / bodyparts which could instead have been butchered. Or vermin remains with which you planned to do something else. Therefore, I recommend to turn it only on if you actually need either space in the stockpile, or ash.
