Sorry to hear of your loss… that is just something that is hard to get over. In regards to the gate, since you don't have a photo of it, it is hard to tell what to do. But you most likely need a door made of hardware cloth over a 2 x 2 wood frame or such, and then with a 'fixed' frame of wood you can build and or plug up the hole the offender used to gain access to your birds. It is somewhat scary to see how little a hole can lead to disaster. Many folks live in bliss, never knowing the same could happen at anytime, should the varmint chose to visit them.
Anyway half inch hardware cloth and lumber with an eye to a tight fit, will go a long way in protecting your flock in the future.
Best to you as you repair things and begin again. You will have a much sharper eye in light of the incident, let this be the last time your flock is harmed in the run/coop.
Regards,
RJ