The best way to cope with this is via the version number of your course format.
Make sure that when you update your course format from 2.2 => 2.3, you only increment the minor version number for the 2.2 version.
e.g if your latest version on 2.2 was 2012040100 and your first Moodle 2.3 verison was 2012071000 then make sure that the next update to the 2.2 version is 2012040101, then 2012040102, etc. Whilst your 2.3 version can stick with the normal YYYYMMDDxx scheme.
That way you know that if the version number in the upgrade is less than 2012071000, then they are upgrading from 2.2. If it is greater than or equal to 2012071000, then they already had the 2.3 version.
If you combine that with the $plugin->requires variable in the 2.3 version, then that should make sure that no one will be intalling the 2.3 version on Moodle 2.2.