It's because she still blamed Cate for Andre's death. That's why Polarity telling Marie to stop chastising Cate over it was significant, because that's Andre's
father telling Marie it wasn't Cate's fault, but himself.
Marie choosing to heal Godolkin is because she was confident that he could stop Homelander. Plus, she was under the assumption that Godolkin being held as a hostage in the hyperbaric chamber would make him want revenge against Cipher. Yes, we as the audience knew that Cipher=Godolkin, but none of the characters had any reason to believe that after Stan Edgar said their ideologies differed:
Stand Edgar: Where they differed, Godolkin believed that he could control Supes, while Cipher, no such thing.
From the aforementioned (being trapped in a hyperbaric chamber) standpoint, they thought Godolkin's body was being controlled, not that Cipher was actually Godolkin.
Also, Marie in Ep 7 responded this way under the possibility of healing Godolkin:
Godolkin might be even more dangerous.
Marie: I don’t think we have a choice.
Most of this is hinging on Marie's hope of taking down Homelander, who she 100% despises more than Cate. Yeah, Cate betrayed her in Season 1, but Homelander is the whole reason the following happened:
1. Getting put in Elmira.
2. Andre dying (Homelander has indirect cause, but still his fault)
3. Being chased by Supes for months after escaping Elmira.
4. The whole Supe Supremacy stuff being pushed. Also, the dude's a monster, and she seemed to understand Shetty's motivation in Season 1 for wanting all Supes dead.
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Lastly, her sister being there, the whole "your destined to become the strongest Supe" stuff and the fear that it brings is lowkey messing up her judgment, BIG time.