My suggestion is to "tweek" auto butcher to not "kill" frames, paintings, and minecarts as these are items used for decoration and are not likely to induce noticeable lag. Minecarts being made of iron are relativity expensive to replace on an almost daily basis.
As well all know these items crash the server. The butcher really tries to kill all lag made. Such as frames, we are all notified that they will get auto butchered in a few days no need to. As well if you'd like to make minecrats as a decoration I advise to make it a temp area to place these minecarts.
If I am not mistaken, I believe the butchers kill all entities. Item frames, pictures, minecarts etc. are coded as entities so there is not a whole lot that can be done to change this from the server side.
Yes, really. This is not something the server can control. It's like asking andrew to allow stone picks to break obsidian... Paintings ect are coded as entities, aka, it's just like butcher killing chickens.