If all colleges and universities were private, I would completely agree with you.
However....When government makes these decisions in their government institutions that are supported with tax money, these government universities run smack into the First Amendment. Government is not to establish a religion. When government rejects Christian courses then government is favoring and establishing an atheistic religious worldview and penalizing those of this sect of Christianity.
You are completely correct these Christians made the wrong demands. They should not have demanded that government give them credit for their courses.
These Christians instead should demand that all government schools be privatized. Do this and there is no opportunity for government to establish one religious worldview of some citizens and trash that of others.
Please remember that evolution is merely one in likely thousands of ways that government in its schools favors and establishes one religion over another.
Government is NOT rejecting Christian courses. Universities are rejecting course that teach false science; false science that is not even supported in the Bible or by many Christians.
To take that on that belief I would have to accept that evolution is a religion; it is not. It is an accepted scientific theory that has been pretty much proven in part and still tentative for other tenants. Religious beliefs have no place in a scientific area of study. There are plenty of religious beliefs such as the great flood and the exodus from Egypt that have a firm basis in historical and geological fact although the bible may not portray the events as they actually occurred. Creationism is not a science any more than scientology is a science. This does not mean that scientists are anti-christian or non-believers. I and many I know are firm believers, but do not take the bible story of creation as anything more than a way to convey a concept of God and creation to ancient peoples who could never grasp the concept of time spanning several billion years. I see God’s hand in the big bang theory, evolution, that God gave one of our ancestors, maybe descended from a near-ape, the spark of soul, free-will and conscience which man could use to learn from and discern the many miracles that God created over unfathomable time. God is not so limited and has no need to limit creation to 7 days. Gods will and meaning is not knowable by man but he gave us the ability to discover the greatness of his works. The bible as written and rewritten by man is a limited view that offers good lessons and admonitions for how we live our lives but not necessarily a literal view of God and his masterwork. The new testament tells us how to find peace in God outside of the old testament, but even those books written by people who knew Christ differ on the same stories and were selected, translated and rewritten by man. Worship God and his great works and not a book compiled by man. Discovering new miracles in the great works of God’s universe makes most scientists more fervent believers because we can see that the universe is not random but is ordered and planned by a greater hand than ours.