I agree with both of you. To paraphrase Claremont, as one aspect of Jean—a multitudinous being if there ever was one—was fragmented and dying, another aspect of her reached out with all her heart to Scott to comfort him, herself, or, perhaps, both of them. This notion that she's had no agency when, in reality, she made it possible for Hope and Exodus to bypass the White Hot Room's safeguards by imbuing the former with
her fire (Hope admits as much in
X-Men Forever #2) and has been in what amounts to a meditative state, repeating the mantra "NowAndForeverNowAndForever" throughout, is puzzling.
In fact, Simonson's
Jean Grey implied that she was safeguarding Phoenix deep within her own psyche or being since the two are inseparable. One can even argue that this is what prevented the White Hot Room—the heart and home of Jean and Phoenix and the center of all creation—from imploding. She may not have been
obviously active, but readers with basic knowledge of Phoenix, the White Hot Room, and spiritual or metaphysical concepts and states should recognize that she was operating on a level that transcends mortal actions and communication. After all, she never truly died. Even after Mother Righteous stabbed her, she continued repeating her mantra, as if by doing so she was holding everything together.