Making his life harder if he doesn't. Things like friendly warships "misreading" his IFF, or shipments of supplies going missing, or a loud "SHOOT ME" broadcast from his fighter that draws missiles like a bug lantern.
The idea is that accomplishing the altered objectives generates a value related to that objective's worth in points, in one of several ways. Either in one absolute variable, which covers general adherence to the altered instructions, and is either positive or negative, granting either positive or negative effects, or in two variables, one of which measures completing objectives, and one of which measures ignoring objectives. Having a higher complete score would grant bonuses (or take away penalties), while having a higher ignore score would make life hell.