Let me give you some details on a few of your points:
@Tom has discussed on streams that he would like this to be something the Geomancer can do, but at the moment, you are correct that there is no way (without a mod) to do this.
You can! You can open the in-game console by typing Ctrl + c on your keyboard, and use the destroy command to do so. Make sure you have selected the object/hearthling/building you wish to destroy before hitting enter. There are many other commands in the console as well, like reset is someone is stuck, im to instantly mine an area, and ib to complete a building. Note that using im will not give you any resources, and using ib on a building can cause issues with things like removing buildings. We would very much prefer that you upload the template of unbuildable buildings to the thread I provided to you earlier before using ib, or else the game won’t be able to improve~
These tend to happen when the AI is overwhelmed. If there is too much going on for your Hearthlings, sometimes the AI gets “stuck” trying to decide what to do, but never making the decision! You can sometimes deal with this by pausing the game to let the AI catch up, or by saving and reloading. If you have specific saves that have major issues, creating a topic in the #support:performance category and uploading the save is always appreciated.
Where the “random stock piles” filtered to prevent animal parts from being stored? If you have multiple stockpiles that can accept an item the Hearthlings will generally select the closest one, even if there is a stockpile that only accepts the item.