I can understand not infecting the passerby from a meta perspective. The result would have been a Prototype or inFAMOUS-style story, which would have been spectacular but would have required at least a two-parter just to fit in the necessary parts of the story. As two-parters are not allowed, that's understandable. But they could have fit in Black Widow getting "ill", though. There's no excuse for that particular plot hole. Her helmet was off, there was a flu, she should have gotten infected. And, as we agree on, it would have given the final battle more tension and give Natasha a chance to show off how heroic she is in a meaningful way, if she opted to save the team before saving herself. And Laura Bailey would have been able to pull off a Hulked Natasha. Have you heard her Halibel voice from Bleach? Laura's voice can go DEEP. I thought she would have been an ideal She-Hulk casting before SMASH and AA because of her Halibel.
I mean, you can see it, Natasha, losing control, manages to save the team members one by one, but at the end, on the verge of losing herself, finds she can't take the gloves off without destroying them. She's doomed to lose control or suffer the fate she saved the team from, gamma explosion. Hulk says a variation of "forget it!" takes the gloves off of her, damaging them in the process but curing her with the damaged gloves, but they are fried from curing Widow and the damage Hulk did getting them off Widow, making them useless. It would have solidified that Hulk/Widow bond they were going for in the script as well.
It is surprising that Red Skull and MODOK were behind this, not Abomination or Red Skull. The Leader in particular would have been useful in this plot, The Leader would have helped Red Skull figure out what would make Thor immune as you said and change that, thus avoiding that particular logic failure.
Thor should not have been affected. "An Asgardian has no need of such protection". My guess the reason why they went against that rule is 1. laughs, and 2. to avoid redoing what EMH did with Thor being unaffected by gamma radiation. Problem is it contradicts the books.