[gvb]

That makes even more sense. The waves would be slamming the ship onto the bottom which would be attempting to drive the rudder through the ship every time. This would threaten to break the ship up very rapidly.

By cutting the rudder free, it would no longer be breaking the ship up, but it would leave a major hole where the rudder post came in, resulting in scuttling the ship.

[dx211]

I think the part about "scuppering" is just some nautical-sounding nonsense that the author of the article threw in. If you read the account I linked to above, it's saying they jettisoned the masts, then cut the rudder, then threw the cannons overboard, but despite these the ship eventually broke apart. Like you say, it sounds like they were trying to stabilize it to reduce the damage, but my impression is they were trying to make it lighter and less top-heavy rather than intentionally sink it.

[Angostura]

In British English if something is 'scuppered (often someone's chances) it is destroyed or sunk. I assume the author was going for this verb usage.