If you use the ext rom unlocker found here
http://www.ppcgeeks.com/how-to-custo...ht,unlock.html
( I think its there anyway.)
You could copy all of the files over to your pc hard drive should you need them, then delete them from your ext rom.. And they wouldnt install.
To keep them from getting installed by custom rom packages you can delete the ms_.nbf from the folder and it wont install that custom rom.. you can also move any files you may want to install later back, or just install them from your card.