The German Bishops Conference ordered an investigation into the German catholic church's history of child abuse (after a researcher in Munich found that there had been 9 times as many cases of abuse there as the local bishop officially knew about). They contracted the Criminological Research Institute of Lower Saxony - an independent research institute - to go through the files of the last 60 years for the entire country - a three year project and an attempt at repaiting their demages reputation.
There were differences of opinion between some bishops and the head of the research center, Christian Pfeiffer, related to certain contract terms of different versions of the negotiated agreement (according to Pfeiffer the results have to be published in any case because many of the researchers are PhD students who need the publication in order to get their degree - on the other hand Pfeiffer also says the data protection concerns are made up because sensitive data was at no point going to leave the church and that he was fine with that but that some bishops didn't belief this; he claims the church added conditions to the agreement at a later point which the church denies while the church allegedly insisted on preapproving publications - supposedly due to data protection issues which are taken very seriously in German). Both parties acuse each other of lying and breaking the contract.
The church decided to terminate the contract with the Criminological Research Institute and contract somebody else. They claim they just don't want to work with Mr. Pfeiffer due to personal differences and will get somebody else.
Pfeiffer did not "publically resign as a matter of conscience", he was fired.