Earlier quoted context omitted.
A few botters don't hurt Pokémon go. But when it's easy to bot, lots of people will bot. It's easy to circumvent anti root, but it's impossible to use the same way for lots of devices without niantic being able to block it again. So it really makes sense for them to go this way IMO.
Not really. It doesn't matter if the phone is rooted or not, what matters is whether it is feeding false gps data or not. Bots will soon find a way around this (non-rooted) restriction anyway. That said, proper protection against cheating would involve using markers (other phones?) in vicinity, so it should be possible too.
I don't condone Niantic's behavior, but I understand it.