Every[1] reputable[2] source[3] I[4] can[5] find[6] (literally just the top search results for "stallman resigns" that have any info about the reason) says that Stallman resigned over his comments defending a fellow computer scientist over his participation in the Epstein scandal. Do you have a reason to believe otherwise?
1: https://www.theverge.com/2019/9/17/20870050/richard-stallman...
2: https://www.forbes.com/sites/jasonevangelho/2019/09/17/richa...
3: https://techcrunch.com/2019/09/16/computer-scientist-richard...
4: https://www.vice.com/en/article/mbm74x/computer-scientist-ri...
5: https://www.washingtonpost.com/education/2019/09/17/computer...
6: https://www.cnet.com/news/computer-scientist-richard-stallma...