This Judge is saying it's not patentable but he did not say that a specific implementation could not be copyrightable. If someone reverse engineers your software and then re-releases it as his own I'm guessing you can still sue for damages.
Exactly. There are many protections available, and even if one specific protection isn't available to you in one situation does not mean that all other protections are also unavilalbe.
Also, in the full ruling note that the "software patents" they are referring to are basic addition of doing something on a computer. Note that if you still create an original process then a patent is still fully acceptable. If someone were to figure out some amazing new sorting algorithm or amazing new pathfinding algorithm or whatever, the patent on the process is still acceptable; what isn't acceptable is taking something and adding "On a computer..." or "On the Internet..." If you create a process then it exists on a computer and off a computer, anywhere you can do something.
Specifically they write in the ruling that the '610 patent is an "On The Internet" addition, the '142 patent is an "On a Networked Computer System", and the '050 patent is an abstract idea with the expected results (receive identifiers, test for a match, output values responsive to a request). The first two were shot down by the SCOTUS with the Alice ruling, the last one shot down forever ago.
If you make a new process worthy of patent protection --- meaning a process that is non-intuitive, or that gives unexpected results when applied -- those patents are still valid even if you happen to implement them on software, they just need to be applicable as a process generally.