I fail to see the connection
I'm sorry, but I fail to see the connection between the GPL and the kind of abuse of human rights you're talking about. If a government or a large corporation wishes to censor information, they certainly have the capabilities to do so in-house. How would adding a 'be nice' term to the GPL affect all the non-GPL software they would use instead, assuming of course that they honour the terms of the license anyway?
And all that is aside from the points already made about the meaning of "free" in free software, and the practical difficulty (impossibility?) of clearly defining what you mean by 'nice' behaviour.
"If it works, don't fix it"
I could believe that either way works. I migrated from RISC OS (which rigidly uses application directories) to Windows (which vaguesly uses application directories) to Linux (which doesn't) The largest problem I had was with Windows, as there were no rules about where apps went, so it was impossible to be sure that you had fully weeded out any given app. MS Apps were possibly the worst for this - ever tried to de-install IE?
Also, what about a hybrid system? When dealing with a particular app you firstly have to ask "is it old-style or new-style" before the next level of searching, which _increases_ the overhead associated with a task.