Trick question, because goodness depends on motivation.
The actual Matrix is the Establishment: The System: the world of Governments, Institutions, Corporations and Media... This Matrix is certainly evil in motivation and effect. And The System is currently being (mostly) destroyed by the Establishment.
The System has been decisively turned-against The System - in what The System itself calls a 'Great Reset'.
So far this year of 2020 the economy has been (?one third) destroyed, government is totalitarian, the bureaucracy penetrates everywhere; and destroyed also are most of the arts (concerts, plays, museums, dance, singing...), science (because research is either stopped or crippled), and almost all of human society (families are legally separated, forbidden to meet). Nothing is unaffected.
One might assume that this is a Good Thing? The System is evil, therefore (it might be supposed) its destruction is spiritually beneficial (even if the physical consequence is that maybe billions will die of starvation, disease and violence).
Does it really matter how or why the System ends?
One clue that it does matter, is that it is the powers of evil who are actively engaged in destroying The Matrix: evil forces are leading the destruction.
Why would They do this unless They believed that the outcome would be even-more-evil?
And the answer is - as always - in motivation. The evil System is being destroyed for evil reasons; evil because dishonest (based on Big Lies, ferociously defended and asserted); because the motivation is selfish; is based on fear, resentment and despair.
Ultimately, because the forces destroying The System are on-the-side-of Satan; directed-against God, creation and the salvation of Men.
When evil fights evil, the outcome will be evil - whoever wins.
Only if The System was being destroyed for motivations that were Good and were themselves spiritual (not material), and God-allied - motivations that were loving, beautiful, virtuous...
Only then would destruction of The Matrix be expected to lead to good - that is to Godly - outcomes.