Within ~/logs we can simply create an empty hidden file owned by root and unwritable by anyone other than root. User can't delete it, thus can't delete the directory. He can still move it, of course, so it doesn't prevent malicious behavior, but it does prevent the user from accidentally doing something stupid.
As is often the case, the TextDrive guys came up with the idea (or at least blogged about it and made me aware of it):
Anyway, it doesn't remove the need for the log writer script, but it does make it harder for the user to make a mistake and is probably worth adding to the default skel setup process.