Hi Phyll
You will see many things on your trip to Egypt and yes there are some issues with animal welfare, accept that you may see some live animals in markets that are going to become food, don't want to be graphic but the food is much fresher than ours when they buy it
Don't go on one of the horse and carriages called a Kalesh, this is applies to all Egypt not just Cairo, other than being realistic and understanding that there are some differences in regards animal welfare there is nothing to stop you visiting Cairo, you most probably wouldn't even notice any welfare issues.
So most definitely go and enjoy
Graham