Origen (185-254): Declared a heretic and much of his writings destroyed.
A prolific and interesting writer on biblical themes and an early source for questions of how Biblical interpretation should be done. Much of his work is lost to history. In destroying his writings, the church lost a great scholar.
Evagrius Ponticus (345-399): Writings condemned and many lost
The early "desert fathers" are the originators of Christian spirituality. Ponticus was in some respects the father of that, and an early and discerning writer about the struggle to overcome sin. Christianity suffers from a lack of an active spiritual tradition to this day.
Heloise and Abelard (12th century): Castrated, separated, vocations denied
Two of the brightest lights meet and fall in love. Together they could have inspired each other to great work, and great work specifically on living together as a couple. Instead the church castrated him, forced her into a nunnery, made both of them perform jobs they didn't want and weren't suited for. And then, even after their death, uprooted their bones more than once out of weird obsession with sexuality.
The Syllabus of Errors of 1864: condemnation of rationality
Pope Pius IX issued this condemnation of separation of church and state, freedom of religion and various versions of rationality, liberalism, and progress. It defended scholastic theology and the traditional power and political rights of the Roman Catholic church. It maintained that salvation could not be found outside the Roman Catholic church. Even if some of its statements were meant more narrowly than might first appear, this became a rallying cry for all those opposed to the age of reason. Perhaps it was de facto overturned by Vatican II.
Excommunication of Leo Tolstoy (1901)
Excommunication of Nikos Kazantzakis (1955)
It goes without saying that one can fill several volumes with scurrilous, pathological, criminal incidents from two thousand years of church history without ever coming face to face with the holy. That is the task of a lifetime. -- Hans Kung, Christianity, p.5
Especially the practice of burning people alive that were considered heretics. And also, the 'gracious' generosity that if a 'heretic' would confess and proclaim his faith in Christ, then he would be strangled before being burned, so that he could die quickly. (Brian Moynahan, The Faith, p.448+)