It appears there are two independent clauses. These could grammatically be stand-alone sentences:
More than half the roster, including such popular characters as Black Panther, Scarlett Witch, Star Lord, Spider-Man, and Doctor Strange weren’t merely killed.
They were wiped out of existence with the snap of a finger.
Is a comma appropriate to separate two independent clauses?
Strictly speaking, maybe the author should have used a period, semicolon, colon, or dash instead.
However, these two sentences are so closely related to each other that a comma seems preferable.
"including such popular characters as X, Y, Z" is an attributive clause. This attributive clause doesn't contain the verb phrase "weren’t merely killed". The verb "killed" refers back to the main subject which is "half the roster."
For example: "The whole group, including Fred, went sailing."
Who went sailing?
"The whole group".
The verb "sailing" doesn't directly apply to "including Fred" (or "including such people as Fred"). The part "including Fred" isn't the subject of the verb.