how about the best of both worlds, install the framework in the php include path with a directory name like Zend_Framework_1.0.2. Then in each clients space you can create a symlink to the version that client is using. When a new version comes out install it in Zend_Framework_1.0.3 and update your symlink when your ready.

This way you can have multiple versions of the framework available to all clients with only one actual copy of each version. Each client can use any available version on a client per client basis. You can easily roll back to a previous version by updating they symlink again.