I wouldn't say you did not perform your job at your best. What does the best mean? not shooting the mother and baby yesterday as part of your decision process considering the final outcome is the one you've been hired for is correct according to me.
You managed to keep the animals away, you killed one of them which was seen by the others who probably will be keeping that experience in their memory for a while. You have no idea how and when they may come back to try to go over the property but you did what you have been hired for.
When working or doing any task, we need to do so being comfortable, making sure we do the correct things according to our common sense, otherwise, after a while, we can not perform at all.
Yeah, well technically I did my job, those kangaroos hopped away but in truth the farmer would have wanted them downed. It's ok, I go regularly so they'll eventually get dealt with if the jump the fence. If not they will live happily ever after.