"ആധുനികത വന്നേ പിന്നെ ആണ് ഇതൊക്കെ ഉണ്ടായത്. " Weak analysis tending towards falsehood. Religion is the outcome of a search for answers by man for his deepest questions on what is life, what is a life worth living, what explains the world we see around us and what is true. Christianity is one answer based on the experiences of a tribe in modern day West Asia which later was taken to the far corners of the world where again conviction in the answers grew on account of lived experiences as well as historical and philosophical analysis. Within Christianity itself, you will see that faith does not confer sainthood on the person. Case in point, there is only one person in all of Bible whom God called as a man after his own heart, that was David, a man who was guilty of murder, adultery and disobedience to God. So, the Christian claim is not that the Church is guiltless (in fact, the weekly confessional that most Churches have would suggest that the Church is a congregation of sinners and not saints). Other religions, Hinduism for sure and perhaps Islam as well (I am not very informed about the Islamic Worldview) are equally important answers and have their own histories of how those answers play out in the world.
Coming to some of the specifics of the message above like Crusades, Galileo, Inquisitions and William Tindale.....as I said above, there is no intent to paint the Church and its actions as all clean and pure. The Church acknowledges errors of the past and it is not a modern day phenomenon. Let us not forget that Martin Luther was a priest who pointed out the error in doctrinal positions, let us not forget the numerous schisms that arose over multiple centuries leading to the formation of a number of autocephalous churches across the world. Or even better, remember how the Nicene Creed that most Christians recite every week came into being.
However, to take the point about Galileo alone to point out the error of picturising it as a Catholic Church's error(I am not a Catholic by the way, Mar Thomakkaaran aanu). The Church then was only taking a position that was held by the scientific community of the time, namely Ptolemy's position on geocentric cosmology. Heliocentricism was a new thing then and there was little scientific evidence to back it given the development of measurement technology. The rest was brute politicking by the Church. (For more details, refer to Thomas Kuhn's The Structure of Scientific Revolutions). However, it is not something that only the Church is guilty of. It happens in modern secular worlds as well. A good example is that of Ignaz Semmelweis, a scientist who contributed a breakthrough to child birth in hospitals was killed in a mental asylum. If you want more current examples, check the current universities and their academic research grant process, you will find very similar politics even today in thoroughly secular institutions. Again, what is to be kept in mind is that it is a very human error and the Church does not claim to be immune from such errors.
Coming to the point about separation of powers. That is something that we see in France and I suppose only in France is that so clearly seen. Take the protestant countries like England; Church of England does consecrate rulers of England. In the US, there was never a period of rule by the Church, however, much of what we see in the US is a result of Christian activity, including almost all of its Ivy League Universities, its Anti-Slavery Movement, its Declaration of Independence itself. So, separation of powers sounds like an idea, however, it is not like one fine day the church and state was split and suddenly you had enlightenment. It was a slow meandering process spread across centuries in many states. (Check The Third Pillar by Raghuram Rajan).
As to Pope's liberal humanism, it is a mistake a lot of liberals made. In the initial days, one got the impression that the Pope was being liberal. That was an error in understanding the Pope, Liberalism and Christianity. The Pope was never speaking as a liberal humanist. He was speaking as a Christian. Check the recent 20 point encyclical that is available on the Vatican website. it is fairly obvious. People confusing liberal humanism with Christian message has a reason. The quote below from Jurgen Habermas will tell you why. "Universalistic egalitarianism, from which sprang the ideals of freedom and a collective life in solidarity, the autonomous conduct of life and emancipation, the individual morality of conscience, human rights and democracy, is the direct legacy of the Judaic ethic of justice and the Christian ethic of love. This legacy, substantially unchanged, has been the object of continual critical appropriation and reinterpretation. To this day, there is no alternative to it. And in light of the current challenges of a postnational constellation, we continue to draw on the substance of this heritage. Everything else is just idle postmodern talk."
Which brings me to the last point. Christianity is one of the largest actors in the past 2000 years and even today defending ideals like love of the agape kind, forgiveness and justice. Stan Swamy is an example, the numerous schools and hospitals that dot countries like India is a testimony to that. Our own WhatsApp group is a testimony to that.
Similar arguments can be made about other religions as well. Civilisations have been enriched by religion and it will continue to be enriched by religion.