Had my sit down today with the shop manager and it went somewhat well. They are going to replace all 4 pistons, valves and head on the right side of the engine. While the pistons are removed that will check the block and all the internals. Then they will compression test the engine, if they cannot get the correct compression the engine will be replaced. If there is any other damage found then they will just replace the engine. If after all repairs are made and there are any issues, they will replace the engine. They gave me a 2012 Malibu as a loaner.
I still think at this point it would in everyones best interest to just replace the engine now. The shop manager said that he will get together with the general manager of the dealership to try to push the issue for a total engine replacement.