REALLY like dawgofdawgness's advice here
The point about specificity is really good -- I think in scenes like it can really help if the villain hits a nerve. Like, if your character has no doubts about doing the right thing, and then the villain comes in like "AHH, BUT WHAT IF YOU AREN'T DOING THE RIGHT THING??" and there's no real reason for the protagonist to believe it, then we feel frustrated if the protagonist is so easily pushed around.
But if it plays into her personality, that changes how we see it. We understand why this argument got to her -- because it's something that she doubted in herself. If the protagonist seems to be oversensitive and it's just to push the plot forward, it's just to wring emotions out of us by contriving a moment of doubt, that's when we we don't take it seriously. But when she seems oversensitive to this point because of the things she cares about and the doubts that she has, then it's a chance to get to see this specific character more closely, and it matters more to us.
I really like the argument of "you're only helping the people you care about, you're only helping so that you can see yourself as a good person" -- that argument works REALLY WELL if that hits something that the protagonist themselves is unsure of. Am I not helping enough? Am I just helping people I care about, or doing this so that I can think of myself as selfless? Is it all about me? She doesn't even have to voice these doubts out loud, but if it hits something that she's insecure about, it's much stronger.
On the other hand, if she's already very confident that she's doing good things, her self-image as a good person isn't really something that keeps her up at night, and she knows she would stop to help anyone, not just people who personally matter to her, that kind of tactic wouldn't work -- because she knows it isn't true. She might be frustrated and angry at those untrue accusations, but it wouldn't hit a nerve in the same way as something that she worries might be accurate. If she's not actually worried about her motives, then it might be way more effective to lean in more on the Shady Company strategy -- the idea that if she were a truly selfless hero, she wouldn't support these people, but that she's been thoughtless about the actual consequences of her actions, having too much fun Being A Hero to care. How selfish. Then, this character who knows she meant well has to grapple with the worry that, despite her best intentions, she might not have done well.
Take all this with a grain of salt, obviously, since I don't know the details of your story or what you've set up so far! But it's kind of some thoughts on how building these sorts of encounters around your specific character and what would get to them, rather than trying to make it general, can make it stronger. I personally think it's a good idea to worry more about being really honest and true to your characters, to think about what affects them and how to convey their feelings as honestly as you can, rather than trying to figure out how to make readers emotional.
But a big part of making a scene ring true isn't in the scene itself, but in the setup. Some advice I got once on a big emotional confrontation is that the readers need to have enough information to already know how your character will feel. So if the villain is going to confront her with the shady activities of her organisation, we have to know enough about the character ahead of time to know that she would be upset to learn of those things.