Rachel with the help of X-Men understands, she shouldn't destroy the Universe.
While Rachel still has a portion of Beyonder's power, he says:
"Except PERHAPS Phoenix, you are less to me than the Amoeba is to you"
Beyonder's goal was to make Humanity one with the Universe
This is funny,
even with the Power Beyonder gave her, which made her the Phoenix Force and Beyond,
"you are what you are solely because I will it"
"therefore, I require the return of what is rightfully mine, in full"
That's the Beyonder talking about the Power he gave Rachel.
This is the scan you were talking about:
"All that Phoenix experienced..the totality of Life, in ALL it's forms...is now his"
This has nothing to do with her power,
but with how precious even one life is,
Beyonder was overwhelmed by the beauty of Mortal life, even ones that are like less than an Amoeba to him.
Which is why Storm say's:
"We each have our little lives, our destinies, our unique paths to walk"
"I find myself, envying your Humanity...your race is trully blessed"