You've excised, either unintentionally or strategically, a great deal of context, which I will be more than happy to provide:
(1) First, Jean admonished Scott for leaving Madelyne and Nathan, repeatedly urged him to call and return to them, and rejected his advances long after they thought Madelyne was dead. That says everything we need to know about her intentions and how she really felt when she was in her right mind (barely).
(2) Her sister's house had not only recently been bombed, but her sister had also disappeared, along with her niece and nephew, by the time of that exchange. And yet, she still agreed to forgo being there for her own family—her parents, her sister, her niece, her nephew—to help him find Madelyne
and Nathan.
(3) In the middle of her own personal and familial trauma and still reeling from the revelation that she had been betrayed by the O5, who all kept Madelyne and Nathan a secret from her, she weathered Scott practically attacking her while trying to get her to admit she was Phoenix and Madelyne and that she was toying with him. Yes, he was being manipulated, but she was also in a state of severe trauma and couldn't even accept major aspects of herself!
(4) After she finally relented and got back together with him, and they found out Madelyne was, in fact, alive, she tried comforting him and still offered her support to find Nathan.
(5) And then came this, not long before Jean finally exploded, where he tried subtly inculcating her with his own guilt when he was the one that insisted they get back together:
With this added context, it becomes clear why she felt compelled to blame Madelyne, especially considering she was on her side in the beginning: She was feeling blamed for Scott's guilt. He practically tells her so. Not to mention the fact that she was dealing with all of the sh*t mentioned above, i.e., her own crisis of identity, the memories of what she had done as Dark Phoenix, the potential death of her sister, niece, and nephew, and her estrangement from her family. The way you've framed it, she was just a jealous ex who would've suffocated Madelyne with a pillow if she got the chance...
No dice.
EDIT Moreover, when it counted, she was on Madelyne's side every time, including sacrificing her soul to Mephisto to save her and Nathan and to relieve Scott of his guilt.