I hike in the Sierra where pack horses are common. Many of the trails would not exist without pack horses, so I try to keep that in perspective. They are not that bothersome. They move in groups faster than me. When I see a group I step off to the side and let them pass. In a day of hiking I've never crossed more than a couple pack trains. Is there horse poop on the trail? Yes... Was there horse poop in the small summit lake I had to drink out of because I ran out of water? Most probably... I took it all in stride. My worst experience with horses/mules on the trail is when a pack train came right through my campsite at 3 AM.

I don't consider horses/mules a deal breaker. They won't run you over unlike mountain bikes. I guess if I were to choose between two trails and all other things being equal I would choose the one without horses.