Except in an organization with many members, there are bound to be exceptions--like McGill, the Cadmus double agent and Jensen, who defected to the Children of Liberty. Or perhaps someone with no other agenda, who just believes in following orders.
That's very possible and might be what throws a wrench into Alex's efforts to keep it silenced. My point with the original comment was in reference to the YouTuber's belief that the investigation story doesn't have anywhere to go.
With the story that the writers have told so far this season regarding Alex's placement into the Director's position, it appears that they're focusing on her ability to be a strong, capable leader. This means more than just making the right decisions. It also entails being able to pull the team together, have the same goal and same plan to achieve that goal. So far, she's struggled in that area, i.e., the examples you mentioned. I have to wonder if this investigation will continue to explore that concept. Does she have the leadership skills to build the team's confidence in her? Can she influence her team to keep the secret? Is she able to locate any possible dissenters and deal with them appropriately? These are all questions that could possibly drive both her story and at the same time drive Kara's.
So, I disagree with the idea that the identity question is too shallow to propel a proper story because I think there is a basis to not only build more character for both Alex and Kara but, also be topical at the same time. Whether they actually do that and accomplish it is yet to be seen.