At the very least, maybe we should pop the Witch Bomb off on her; if nothing else that would be even more incentive against contracting.
I'd worry that Witchbombing Madoka would make her more likely to contract in order to fix that situation like she did at the end of the original series.
That said, I agree with the feeling that we have been neglecting Madoka and our relationship with her. And she's been the worst victim of Sabrina's overbearing tendency to
manage people. Part of that is us trying not to trample on Homura's feelings and traumas, and so many of those traumas being related to Madoka leaves us feeling unsure of the right thing to do. But another part of it is our tendency to just run with our impressions of people from the show and not dig deeper until we have some sort of epiphany about it.
What I'd really like is to sit down with Madoka one on one, where she won't have to worry about the feelings of anyone else in the room and have a good long talk with her about how she's been feeling about everything that's been going on. She's got a huge amount going on in her head that we haven't been talking to her about at all. I'd like to give her as much information as we can, including and especially the fact that we're holding back information because just knowing it is hurtful to people, including her and her friends.
I'd like to give her our honest assessment of the current situation, where we think we've got a handle on things and where we're weak. I'd especially like to emphasize that we are not lacking magical firepower at all, and that in a fight we're regularly holding back to avoid collateral damage like not accidentally igniting the atmosphere. And that we've been treating Social like the final boss it is. Give her the whole run down of the social dynamics of the local magical girl population and ask her what she thinks we should do. Because Madoka is a considerate, thoughtful person who's good at picking up on subtle cues, and could probably give us a lot of insight into where we've been screwing up. I'd like to run the Ono situation by her, as one example where I'm honestly still confused about everything that happened there, but I'd expect Madoka to pick up on something obvious we've overlooked.
And I'd like to admit that we've been behaving the way we have toward her because we've been worried about making her feel useful out of fear that she'll contract in order to be able to contribute like Sayaka did.
We can be emotionally honest with Madoka without dropping all the infobombs on her, and I expect that emotional honesty to help a lot. Just getting a good sense of where she is in her head and how she's feeling about the whole situation will be a huge deal for us being able to better address the areas she's been agonizing over. And opening up lines of communication will make her a lot more likely to talk to us.
Speaking of which, we should ask what Kyubey's been saying to her behind our backs. It's pretty obvious Kyubey hasn't been anywhere near us lately, but he slipped in to pounce on Sayaka in a moment of weakness, and it feels obvious to me he's been taking every opportunity when Homura's been away from her stalker duties to work on her.