You might not even need to make them slower; if there was just some way to round them up, that would solve a lot of the issues. After giving it some further thought, I think part of the reason why they're so frustrating is because you end up having to hunt them down one by one, even if you have enough speed upgrades to catch up to them easily. And the fun in this game feels like it's when you're trampling a bunch of enemies at once -- it feels perhaps a bit tedious to have to do this little chore of killing each one individually.
Maybe having a little stun if they get trampled on so you can capitalise and kill the one guy without him running away? Or some kind of herd script that keeps close-by fireball casters together when they flee so you can squash them all at the same time?