I think this scene plays more to the automatic rejection of everything that Murph would bring into the house. Lois knows how Tom will not want anything connected to Murph and the scientists brought into their home.
Those scientists had taken their father away from them, and had proven (to that point) to have failed at saving the planet. Murph, having taken up the mantle from a different direction with the same people, only served to remind Tom of what he had lost, and what he thought his family faced. Anything Murph brought with her would automatically also be connected to that same pain.
Lois knew this. She wanted the help for her child, but she knew it would be rejected by Tom because of Murph. This is why she was willing to leave with Murph and the doctor. She wanted her son to live, and she wanted to hope that something could be done. Only by breaking free of her husband and his misguided oppression could she succeed in getting that help.