You didn't have a near miss. It sounds like you actually installed Pages 5.
Pages 5 is in your Applications folder.
Pages '09 is in your Applications/iWork folder.
The problem with Permissions is a different issue and possibly due to you having upgraded your system to OSX 10.9 Mavericks.
Mavericks now lets you know if you are saving to a folder where UNIX (the operating system) determines that you do not have permission to write. This is part of the security in the system. It should let you override the permissions. It is more of a warning. Unfortunately one of those warnings that happens so often you automatically override it ever time you see it.
Unless you have a totally new Mac you may be better not having either Mavericks or Pages 5. Particularly Pages 5 which is a real downgrade from the previous Pages '09.
You can compress (Archive) Pages 5 and not have it bother you. You should also turn off Automatic Updates in your System Folder.
This is an example of features that are supposed to help people who do not really understand their computer being more hinderance than help. You have had things change on you without your knowledge then cause problems you never had.
Peter