Hi,
Sure. Instead of overriding it, just change the name of the plugin to affiliate2 instead of affiliate (you have to change it in the xml and php files and their names too) so that the plugin is not updated when you update HikaShop.
Displaying the affiliate area button only for affiliates will also require the modification of the affiliate plugin code. You'll want to change the code in the function onUserAccountDisplay in order to load the data of the current user and only display the button based on whether the data indicates that the user is an affiliate or not.