It doesn't affect the valour, but if you're not carfeul you might end up with "good runner" or "not so bold" vices which will decrease morale and increase the likelihood of routing in the future, especially where the unit in question is a general (his morale V&Vs affect the whole army).

It's better to withdraw (ctrl-W) rather than rout, though they will be a bit slower about it, and may just end up routing anyway