Usually I hunt them, but if campaign meant to be fairly played, I give them exception (unless they betrayed me ) or not all of them.
it gives no particular penalties, you'll just eventually gain the "bloodthirsty" trait.

true, routers bring less experience than fighting enemies,
In a bridge battle (with gauls for example) this "pig-slaughter" is so massive, that my general immediately gets this wretched bloodthirsty trait, but with plenty of exp anyway