This is a really unfortunate situation we knew was possible during development. We looked into a few possible solutions such as having the blocks maintain physics while being moved or not being able to be placed inside the tower like you suggested. We ultimately did not pursue any of these options as all of them came at a cost that greatly impacted the building freedom of all players creating more small frustrations for everyone. However, our final situation can cause rare and large frustrations due to miss-clicks.
If there was a way, we could precisely tell player intention without bogging down average player interaction we would take it in a heartbeat, but as it stands the overall cost to the average players is too high. If it is any consolation, I do genuinely feel really awful that we caused you any upset or frustration.