if you encrypted the footer links a user might just create a new footer.php just to remove it. but base on my experience this works some how for other wordpress users for not removing the footer links. encrypting the whole theme might be the best but it is overkill i think. if you are looking for encrypting software make sure it is capable to run in different servers.
There's NO way to prevent people from removing the links. There's a simple CSS trick which I won't mention here. We can only make it harder for them to remove the links.
yup a simple css trick and encryption will do. but there are still no guarantee that they cannot remove your footer links.
How do i encrpyt? Is it like add the encrypted file back into the normal theme place and rename "footer.php"?
i believe under the creative commons license you have to leave it so the people that use it can remove it. your code is only allowed to be used and distributed for use with world press if you accept the world press license, and that is all code should be open. do you think people will trust you if you hide links? you can use that to put 500 links that are invisible to people that use it.