Forcing applications to use a separately defined and maintained file dialog is impractical in my opinion. There are lots of ways in which file access can be presented in a user interface.
The problem is rather caused by filesystem layout conventions. I think that a better solution would be to split user home directories into two classes of files: data (that is, files that the user typically wants to see and work with as part of the normal workflow) and "user profile" kind of stuff (.bashrc, configuration files, etc...) that should be "privileged" and require special access rights. These might require interactive confirmation before write access is granted (similar to the split user accounts in Windows with UAC). However, I wonder if these sets of files can be separated cleanly. Marking files as "privileged" should be doable using extended attributes, though.
The problem is rather caused by filesystem layout conventions. I think that a better solution would be to split user home directories into two classes of files: data (that is, files that the user typically wants to see and work with as part of the normal workflow) and "user profile" kind of stuff (.bashrc, configuration files, etc...) that should be "privileged" and require special access rights. These might require interactive confirmation before write access is granted (similar to the split user accounts in Windows with UAC). However, I wonder if these sets of files can be separated cleanly. Marking files as "privileged" should be doable using extended attributes, though.