Here's what I did...

Instead of adding a new option in the upgrader for applying a hotfix, I simply modified the upgrader so that it can accept and handle hotfix TARs as if you were doing a manual upgrade.

So you can run upgrader.php, and on step 5, use the hotfix TAR as the file (URL now supports relative paths if you start it with a /). Just like with an upgrade, the upgrader will extract files as necessary skipping over files belonging to addons you do not have installed or files which you manually edited more recently than what is in the hotfix.

This will be available starting alpha3.

This is probably okay, but I am wary with the idea of making hot fix installation easy. Users need to have a level of expertise so we know they know what they are doing. Otherwise we are giving people enough rope to hang themselves.