He wasn't in control anymore.
Even though he was one of the three founders, and initially co-editor-in-chief, and the most well-known name at the paper, he had already given away all his power over the paper and demoted himself to simple journalist employee (for reasons that elude me) before the time of the Reality Winner scandal.
Other journalists and editors at the Intercept handled the Reality Winner story.
Though there are allegations that Glenn was given the opportunity to call "dibs" on the story, seeing how he was the famous "whistle-blower advocate journalist" and Reality Winner probably only chose the Intercept because of him, but he allegedly refused to take it because he was busy with other stories and projects in Brazil.
If Glenn had taken the story, rather than leaving it to less experienced colleagues, maybe Reality Winner's cover wouldn't have been blown - or so his detractors say.