2007 Nissan Altima Cross fired battery

I took my car for a small dent repair, and they cross fired my battery while they had my car in custody. The auto center then DROVE my car to Nissan dealership due to all the problems. No power, transmission stuck, etc. Nissan had to replace my entire computer system, but stated that my car was running HOT when the auto center brought it them.
After I picked up my car it was misfiring, and I was told that my head gasket was blown.
Can the misfiring of the battery, then driving the car with the computer system messed up. Result in a blown head gasket and fuet injectors? My car only had 39,000 miles and I have always maintained it for my warranty. The Auto shop is telling me that they did not cause this, and I am out over $4000.00 in repair expenses. Nissan also voided out my warranty because the Auto shop worked on my car and caused problems. Was the battery the cause of all the issues I had to face? Thanks