Making it more difficult to actually break the system is a good thing, insofar as it does not actually restrict the freedoms of the users who know what they are doing. I think the fix introduced by PopOS:

To prevent such incidents in the future, Pop!_OS patched the APT package manager. Now, POP!_OS won’t be able to enter “Yes, do as I Say”. Instead, they will have to add a special a file to enable it (if someone really wants to remove the packages).

is reasonable, because the user can override the protection if they really feel they need to (and know what they are doing, of course).