It is against MLB rules to have side agreements about not offering QOs. It could happen, but the commissioner has the power to impose substantial punishment if something like that was uncovered.
The Braves and Santana might have been tempted to collude in this way. But they didn't as subsequent events showed.
I thought players in the past had agreed to contracts or even no trade approvals with the contingent that the acquiring team would not offer a QO (or arbitration as it used to be).