Some people would say that faith and reason are mutually exclusive. They believe that they are opposites: religion and logic are diametrically opposed. If you go around trying to "prove" morality, you lose the ability to just *believe* it is so, because God said so. On the other hand are those who believe that religion and reason will take you to the same place. Descartes, St. Thomas Aquinas, and oodles of other philosopher think that if you're smart enough, you can prove God exists and Christian morality is the way to go.
I am of the opinion that religion and reason are complementary. I think you should use logic to prove what is NOT true, and you just have to use faith to believe what is true. This utilizes the strengths of both approaches. For example, any scientist can tell you it is a lot easier to disprove a null hypothesis than it is to prove that your hypothesis is correct. To prove a statement false, you only need to come up with one counter example. Proving a statement true is much more difficult- maybe there is a counter example that you just haven't thought of yet.
A religion that discourages the use of logic probably has something to hide. If in fact that religion is true, you shouldn't be able to poke holes in it with reason. For example, a cult may say "Don't think about comitting suicide by drinking Kool-Aid and cyanide. Just believe that God wants you to do it." This could easily be disproved. Since God is a loving God, he wouldn't want you to do something so obviously damaging without benefit. Likewise, if say the Oompie Church of Jesus says "Don't use contraception. Don't think about it, just believe that God wants you to do it." You should be wary.