Can a Catholic reject the doctrine of Substitutionary Atonement without entering into conflict with official church teaching?
Since the Church rejects the usual Protestant understanding of Substutionary Atonement, there is no problem in rejecting it. This post addresses the issue well:
Then why did Jesus die?
Did He “have” to die for man’s redemption, or was there another way?
Did Jesus have a choice in the matter?
If the penal/substitutionary atonement theory is unorthodox, what is the orthodox (i.e., Catholic) belief?
The post linked to above contains a link to the Catholic Encyclopedia that addresses your questions more fully. It is true that God ordained that Christ would be crucified, and that He would use the Cross to bring salvation to the whole world, but this is not the same thing as saying that God willed or desired the Cross which is what the substitionary atonement believers hold. There is a distinction: if one says that God Himself willed and desired Christ to be killed, then one is saying that God desired men to sin - to commit the sin of murdering an innocent Person. God cannot will evil like this; He can only permit evil and work through evil, i.e., turn that which is evil into something good. This and the topic as a whole is more fully expanded on in this article by Catholic apologist Mark Bonocore: