Anything that RenegadePizzaGuy said. You also have to take into account that in medieval times there was no "atheism" as we see it now. Yes, there were people not believing in the church, but every had a "system" they believed it. There was simply no hint that there is no god.
Even better than undermining via the kings power would you be to give his subjects a bible in their language (like Luther did, which was almost the end of church) and let them revolt. One of the many reasons people let the church rule them is because they could not read the Latin bible and interpret it. So everything the priest said was a rule of god.
Educate the masses about Christianity, let them revolt, then kill the evil heart of the church.
/edit because I'm kind of mad at the comments claiming I'm wrong about atheism. So the following part is dictated to explaining why there was no atheism in medieval times/
Lets establish some terms. (all from Wikipedia)
Atheism is, in the broadest sense, the absence of belief in the existence of deities. Less broadly, atheism is the rejection of belief that any deities exist.
Heresy is any belief or theory that is strongly at variance with established beliefs or customs. A heretic is a proponent of such claims or beliefs.
Infidel (aka non-believer)(literally "unfaithful") is a pejorative term used in certain religions for those who do not believe the central tenets of one's own religion, are members of another religion, or are not religious.
Agnosticism is the view that the existence of God or the supernatural are unknown and unknowable
Some comments said my statement, at that time there was no atheism, is simply wrong. So i will prove now, that this statement is true
First we start with looking at the counter "arguments":
Diagoras of Melos was not alive in medieval times and Critias too, so what they spoke does not matter to us. Same with the bible, even more because its written about non-believers not about atheism.
Just picking one point in history and then saying, well because of that its safe to say: there was an atheist, so there will be always someone believing in this system is wrong. If i write now a text about my believe in a huge space fish that created everything wont mean that in 800 years there will be a person believing in the same thing.
Critias did not talk about atheism, just about religion is wrong. Not believing in religion does not exclude the believe in a higher force.
Someone trying to prove that there is god with science to combine two systems is not an indicator that there was an actual stream trying to do the opposite.
//edit forgot to include Heraclitus.
Heraclitus was in no way atheistic. His saying the path up and down are one and the same is now the base of many pagan systems where "as above so below" is the center. The statement the path up and down are one and the same in in fact deeply rooted in gnosticism.
So no argument that was brought up is actually valid.
And again to know that there is something like atheism it not the same as to practice it.
Lets look at the world view at those times:
Earth is a magical spinning disc, everything around us is there only because we are. There was no open theory that humans evolved from a tiny cell. Stars were body less lights in the night sky. To actually believe in atheism in this setting is nonsense. Any psychiatrist in this time would call an actual atheist delusional, schizophrenic or just insane.
Just imagine a conversation like: A: I don't believe that there is some higher power! B: Did you look at the sky? How would you explain the magical sphere giving you light each day, letting you live? who makes it rain to provide us with food?
Person A has no logical way to answer and explain why he is thinking like that. Believing in atheism was in no way a rational decision.
Now we look at the people actually believing is something different that the church:
Most of them had some other believe system in place to substitute the church, and practiced it in silence. There were too many different streams of these people to count them. These are the heretics and infidels.
Let's talk about actual educated humans and the scientific community:
Even though under these people it was a fact that earth is not flat, most did not believe in atheism. Researchers at that time had in fact a rather occult world view, based on religion but laced with their opinion on the world(Lets not forget science is rooted in occultism and was always closely intertwined). Many combined different believe-systems.
The closest stream within this community which could be called atheists were Aristotles followers (their research led to evolution theroy). They tried to explain the world with actual science, without considering god or anything like that. If asked if a god exists with would reply with i can't tell you, there could be or just maybe but they would not deny it. It was an agnostic stream of thought.
Feel free to prove me wrong. But until then my statement, that there is no actual reason the believe in atheism, stands.
Lets look at the people in actual power positions and the Vatican.
Almost none of them were actual Christian. Religion and the church was used to establish control, lower tier of the church had only the same information as the pleb and just did want they were told. Kings had mostly little interest in religion, for them it was too only a tool to gain power.
Atheism was not known like it is today. In medieval times there was not even a word for this. It wrong to assume "rational" thinkers turn always to atheism. For the uneducated masses it was rational to assume there is a higher force, for the educated folks it was rational to say they can't know if there is a god, because they could not set up a complete system that worked without a higher force. On the other hand saying that the religion, the standard of approaching spiritualism, is not the right way does not implicate that there is no higher force. In the end actual atheism as we define the term was simply not logical and such a tiny fraction of all people were thinking this way that its is neglectable in terms of general world views. Not to mention people don't want to get killed because they practice a irrational believe, it was not worth it.
In terms of statistical relevance it's the same to say in those times there was no atheism, as to say there is no cannibalism in Europe today.
A quick look at the wikipedia entry of the story of atheism proves my point.
Writings of that time telling that there is no god were closer to neo satanism than to atheism. (Mankind is the higher force of the universe, their own gods)
I believe in the high standards of stackexchange sites and claiming some statement is false, even in comments, should not be accepted if there is no actual to the topic related proof or argument.