Can we disable a
SPJobDefinition for a particular Document Library?
Assuming you're referring to Document ID timer job. This is not possible. Others have went the full custom way and implemented custom Document ID service in order to make this possible.
Their is no such option which you can use and Disable the OOTB timer job service at the document library level.
Timer Jobs perform the task for timer service, web applications etc. If you disable the timer job for a web application scoped then all the site collection from that web app will be suffered...i.e. if you disable the timer job for the alerts then whole webapp will lose that functionality.
Now, if you want do something at Document library level, may be think about the event receiver.