The group of characters resisting God!Sue in the Sueniverse include Buffy Summers, Applejack, Bruce Lee, Xena, Sailor Moon, Optimus Prime, and Superman. Who are among the people most indicated to deal with the situation (probably the others too, feel free to add them if you know why):
Applejack: her fandom is invaded by Sues, with the author implying that Alicorn!Twilight is one she's best friends with and de-suefied her, and, with the help of the other members of the Mane Six, has defeated three different Physical Gods (Nightmare Moon, Discord, and Tirek);
In addition, she's the closest one to being the Badass Normal as she's just an ordinary but reliable Earth Pony.
On top of that, she is the Element of Honesty. Honesty with one's self is a key part of the final confrontation with God Mode Sue, both in how she is unable to lie to herself, and in how her actions reveal her love to be a lie and helps her realize her self-deception about Spock's love for her.
Scrooge McDuck built a financial empire by being "tougher than toughies and smarter than smarties, and he made it square", and is really strong and a capable combatant. By the description he's a Sue... Except he's a well-rounded character, with defects and all. Someone who could have been a Sue but never was.
Hercules is someone who, through sheer determination, defied fate and made himself a god.
Ensign Sue being the one to come up with The Needs of the Many line that brought Spock back from his brainwashing may at first seem shoehorned and (ironically) a little too deus ex machina-ish for someone who no longer with Sue powers, but remember: Ensign learned the hard way the very same thing by watching with clear eyes the destruction the Sues cause to everyone else, and she actually gave up the chance of having her Sue powers back when she betrayed her sisters, as she understood that her petty needs are nothing compared to the balance of the multiverse.
It is also fitting in a meta-sense. Sues, both in general and in this story, warp canon and narrative convention to suit their whims. That leads to characters acting out-of-character and plots that don't make sense internally or conflict with the lore of the parent series. What Ensign Sue does here is convince a character to act in-character and she does it with that character's own line and philosophy. It's basically character re-railing.
Ensign Mary Sue is reborn as Mary Smith at the end of the series. Sues, are, by definition, super-duper-special and fantastic in every conceivable aspect — and their names are no exception. However, over the course of the comic, Ensign Sue gradually learns the errors of her ways and becomes normal — and human. She goes from being perfect and amazing and exceptional to being a normal person; so her being reborn with one of the most common female names and the most common surname is fitting, in a way.
In addition to this point, Smith is the surname of the person who wrote the very first Mary Sue by name in the Star Trek-verse - Paula Smith, after whose character Lt. Mary Sue the trope for this kind of character was named.
Black Hole Sue, defeated the Physical Goddess that was Glory (with help, but she did it), and, in the comics, killed magic by destroying the Seed of Wonder;