Catholic moral teaching, as we all know, distinguishes between acts that are evil in their object -- and therefore are always and everywhere evil, regardless of circumstances or intentions -- and acts that are not evil in their object -- and therefore may be good, depending on the circumstances and intentions.
Among the acts that are not evil in their object are acts that are, you might say, "presumptively evil." Well, I might say that; a theologian might say something like "evil absent a grave reason." I don't know that they are a formal category of human acts, theologically speaking, but a list of them would include:
separation from a spouse
cooperation with grave evil (the graver the evil, the graver the reason needed)
verbal misleading (permitted ex justa causa according to some schools of thought)
divulging private information prejudicial to another [CCC 2491]
And suchlike things.
Now, while the Church does teach that it is up to the actor to determine whether there is a sufficiently grave reason to perform suchlike things, the Church does not teach that the actor can make this determination in any manner he may choose. To the contrary, the Church teaches that the grave reason for which the actor acts is itself subject to objective moral analysis. It is possible to know that an actor -- be it a state in the case of war or a surgeon in the case of amputation -- is wrong in his evaluation of the justification for performing an act that requires a grave reason.
I'll even suggest that a great deal of the Catholic moral tradition is, in one form or another, analysis of the validity of arguments that grave reasons exist to perform acts that require grave reasons. (More generally, it's analysis of the validity of arguments that sufficient reasons exist to justify acts, but acts requiring grave reasons would, I'd say, require more analysis than other acts.)
So it's not really true to say the Church "leaves to the prudential judgment" of an actor the determination of the moral acceptability of an act. The Church only "leaves" us to act under the presumption that our consciences are well-formed in accord with the moral guidance the Church provides. And whether we actually follow well-formed consciences can be known, in certain circumstances, by others.
It's not sufficient, for example, to say of a decision to go to war, "The state knows facts that we do not. Therefore, we can't say going to war was morally wrong." To the extent the argument to go to war is known, it can be evaluated for validity in light of the Catholic moral tradition. An invalid argument does not support its conclusion, even if its premises are true.