For the most part its individual members of organizations, or smaller parts thereof that are responsible for this while the larger organization is adverse to all change. Take for instance individual monasteries sheltering jews during the holocaust while the catholic church cut a deal with the regime to allow catholic schools to continue in Germany.

Likewise, while the church as an organization opposed much of intellectual reform, as evidenced by frequent persecutions perhaps the most famous of which is Galileo but in fact he's just the tip of the iceberg.

The early universities in Europe are in fact predated by similar "academies" in China which are less influenced by religion. Likewise, one has Greek academies which have comparisons to the modern university, but which were sacked during or before Muslim invasions. Furthermore, such universities were often founded by individual monastic efforts, rather than say by papal decree or the larger organization.

Many of the problems you mention that "organized religion" campaigned to end were caused by organized religion.

Also, regarding slavery you'll have to cite the nations, because in the US for instance this was not the case. While many of the prominent anti-slavery figures are men of religion, what religious organization at the time and as a whole issued a proclamation against slavery in the US (a proclamation against slavery in Europe or Worldwide at this point was rather status quo, the US being one of the last of elite nations to have slavery at all).

Some secular organizations are problematic with overseas aid due to misguided values, but so are some religious organizations. For instance, several countries have banned all foreign aid workers because of religious aid organizations who have brought in people who hand out bibles against the express wishes of that country. Furthermore, religion has been organized and providing aid far longer than secular organizations, so it seems disingenuous to blame secularism for the failures of Africa.

Also, Catholicism defined absolutely everything during the time period you discuss. It was involved in absolutely everything and historians often debate whether it was ultimately responsible for advancing or hindering various good or bad events.