The Marvel Cinematic Universe is known to roll with the punches, and shift things around when the need arises.
As far as franchise runs go, the Guardians of the Galaxy duology is a solid two film series that really doesn’t need to progress under anyone else’s auspices.
Without a third film to sully their reputation, the Guardians can serve as an inspiration for the future, without having to weigh it down with unnecessary baggage.
Canceling Guardians of the Galaxy Vol. 3 lets Disney proceed into its future without having to worry about James Gunn ever again allowing the MCU to push forth into the future with barely a mention of his work.