We are not happy about this either. Native Instruments response to this is:
Originally Posted by CHudson
"I know it isn't easy for non-technical users, but there is no other solution. This is the way it will work for ALL KP1 to KP2 library updates, not just Garritan."To make this easier, Tony found a way to a batch file to automatically move the sample files to the right folders. You can find it here: http://www.garritan.com/Kontakt2PlayerUpdate.html It is PC only and we'll look into a Mac version as well.