How does one "negligently" shoot someone that they intended to shoot?
The answer is that homeowner's insurance covers negligent and not intentional acts. Simply winning a case isn't any good if you cannot collect the judgment. That's why the Plaintiff's lawyer pleaded negiigence; so he might be able to collect from the insurance company.
On the other hand, it means the homeowner Defendant gets a lawyer paid for by the insurance company. That beats paying for your lawyer yourself.
As to the civil suit, Texas has a law supplementing its Castle Doctrine. Basically, if you can prove the facts that invoke the Castle Doctrine (in this case entering the home by force most likely) that will preclude a civil suit like this. Oh, it can still be filed, but it can be thrown out fairly easily.