Can we use a Paper Private Key that has been loaded in the Bitcoin client?
1.) The web page at BitAddress.org can be loaded from a file on a thumb drive or other storage.   Most browsers let you save the web page using a View Source (right click maybe), and then Save File to a thumb drive. 

Then from the offline computer you open the file from the browser and the BitAddress page will load.

2.) The private keys don't expire or invalidate after they've been imported into the client. You correctly identified the problem with that is how if you spent any of the incoming funds, the client creates a new address for "change" and thus the wallet may show a balance that includes funds not in any of the addresses from the imported private keys.  So wallet backups are still important.