Maybe Bastion doesn't want them becoming friends, maybe he thinks it will undermine any potential influence he might have, or maybe if they gang up they'll be too powerful together for whatever Bastion has planned. Or he fears Quigly's hate for Alderode might interfere with Duane traveling there (though he seemed pretty set on that).

Bastion didn't seem like the casually murderous type so I hope it is something more than Quigly being a minor complication which his plans would be better off without. I trust he has a real, solid reason for getting rid of him which we are not yet privy to.