Great! You have the safety grounds run separate.
Now you have the ability to easily make the sub-panel ground attach only to the box ground bar for equipment ground.
All panels have the neutral bar isolated from the box, just like the hots are isolated from the box. The only difference is that the main panel ties the neutral bar to the box with a strap or a green screw.
Remove the bonding strap or green screw in the sub-panels.
Make sure the sub-panel neutral is connected to isolated neutral bar and the safety ground is connected to the box grounding bar alone.
And yes if you can afford the GFCI's at the waterers, then go ahead, but eehhhhh......