I would be really surprised to learn that EPA has access to "drones" which to my knowledge are paid for and used by various Department of Defense entities. It's my understanding they don't have enough now for our overseas operations. I would be really surprised to find out they are lending them for use to EPA.
EPA has had their "teeth pulled" lately with the upcoming elections and aren't particularly aggressive with enforcement actions for environmental violations right now. If they are doing this, it would be very surprising.
I wouldn't be particularly excited to have drones watching what I'm doing, but I do love to be able to go to the NRCS office and have aerial photography or satellite imagery pulled up of our land for maps (or get on Google Earth for that matter). In my mind, its a little hypocritical to want it both ways. If its ok for agencies to provide me with imagery that useful for my purposes, it ought to be ok for them to use it for their purposes. ALL resource agencies use aerial imagery - sometimes acquired by airplanes - for all kinds of purposes. Many cities make extensive use of aerial photography.
If EPA is doing it (which I doubt), they are likely using it to inspect PERMITTED confined animal feeding operations. When you get a permit, you give the permitting agency the right to inspect your facility unannounced. The method is up to them.