When you try to use reason to understand things in the Bible or Religion, a lot of people will bring up the faith is a matter of the heart not the mind, or something like that, which is a discussion ender. I'm not necessarily talking about the creation - evolution debate or politics and religion, but things like the Inerrancy Debate, What does it take for salvation, ...

You can't explain or prove religion by reason as Blaise Pascal, who was a lot smarter than I, tried and eventually gave up. Others have tried also as indicated in the introduction to this section.
Certainly religious belief relies strongly on faith which involves the heart.
Pascal's famous quote (sometimes attributed to C.S. Lewis who said something similar) is, "There is a God shaped vacuum in the heart of every man which cannot be filled by any created thing, but only by God". See Theology for what he actually said.
But, that doesn't mean we should not have rational discussions about religious or in particular Christian dogma.

Here are a few thoughts.

I think that in many cases using the association of the heart with love and compassion to subconsciously gives credibility to a position which may be hard to defend rationally.
This is what I have to say about that.
We all know the Exodus passage "Yet Pharaoh's heart became hard" [Exodus 7:13,23]
There have been books written and sermon series taught on the rebellious heart, e.g. "A stubborn and rebellious generation, whose hearts were not loyal to God". [Psalm 78:8]

How about the science?
Here again, the heart isn't always good.

There are countless examples of people getting in trouble by allowing their emotions, whether love/passion or hate, to override reason.
Dr Paul MacLean's research at the NIH showed that the the reasoning part of the brain (Neocortex) can be hijacked by the emotional parts (Limbic System).

In ancient history people thought the mind (control over the body and thinking) was in the heart and the brain was for cooling the blood. Although Hippocrates proposed the mind was in the brain and not the heart in the 4th century BC, it wasn't until the 2nd century BCE that Roman physiologist and anatomist, Galen proved it was in the head with his Squealing Pig experiment.
So, the mind and heart may have been synonymous in the Bible.

We now know that the emotional (heart), part of the brain is in the Limbic system (Hippocampus, Cingulate Gyrus, ...), located deep inside the brain. This part we share with all mammals.
It is associated with love and compassion, but also the source of many addictions.
People need to use their cerebrum to resolve that urge from the limbic system for a banana split and settle for a sorbet for desert.

What God gave humans to distinguish them from the other animals was a large cerebrum (neocortex or outer brain) which we use to mediate primitive feelings coming from the inner brain.
So, why shouldn't we use the tools God gave us to try and understand him?

Wisdom:
Another rational conversation stopper is Luke 10:21, "I praise you, Father, Lord of heaven and earth, because you have hidden these things from the wise and learned, and revealed them to little children".

Wisdom isn't always bad. Colossians 1:27-28 says,
"To them God has chosen to make known among the Gentiles the glorious riches of this mystery, which is Christ in you, the hope of glory. He is the one we proclaim, admonishing and teaching everyone with all wisdom, so that we may present everyone fully mature in Christ."
Most people think this was directed at the self-righteous Pharisees who had added all these laws outside of the Bible, and felt superior because they were the experts in "the law". Jesus was constantly confronting them.

Of course there is the greatest commandment,
"Love the Lord your God with all your heart and with all your soul and with all your mind and with all your strength." [Mark 12:29-31, Matthew 22:37, Luke 10:27]

Your heart is important:
I'm not saying to ignore your heart. Two icons of American Business had this to say about that.
Steve Jobs in his famous Stanford commencement address said,
  "Have the courage to follow your heart and intuition."
Carly Fiorina in her MIT commencement address said,
  "You have to master not only the art of listening to your head, you must also master listening to you heart and listening to your gut."

Links:
How to Make Your Heart and Your Mind Work Together :zenhabits
"The Heart of the Mind", 2011, Jane Katra and Russell Targ
Faith and Reason