Had a bit of a fridge-door realization;
this is literally the Deus Ex Machina
think about it; a literal god descends from the heavens to solve the writer's unsolvable problem (how can we kill Woundwart & his army, without killing anyone? because kid's show) quickly and completely to lead to a happy ending?
I didn't like the ending if I'm to be honest, but I can't dwell on that because I can't think of a better way to end it.
That said, this ending hurts the rest of the series, as it destroys the "morally grey" aspect of life and it destroys the "faith" part of the rabbit's religion.
When the writers had the Black Rabbit descend down and deliver righteous justice to Woundwart's regime, the writers are essentially offically declaring that Watership Down is righeous, and that Woundwart's army were hubrisic sinners. With that, the writers have dumbed the show down to just Good Guys vs Bad Guys. Which is a bit of a turn around considering the intrepid action the writers took at the end of the second season, when Woundwart was about to give up and offer peace, but Hazel & co. destroy Efrafa anyway. This built Woundwart into a believable character, and also challenged our assumption that Hazel was always fair and pacisiftic; it made Hazel look like a struggling leader doing what he thought was right, as opposed to what is right. Suddenly, he's not the perfect hero! Flaws! What makes a story great! But when the Black Rabbit comes down to saves Watership Down and destroy Woundwart, it means that Watership Down was always and objectively right - the writers burned down this degree of depth and struggle to the characters. The original had the dog released, which was just another witty defense idea that the rabbits came up with - no righteous and devine judgement, just rabbits protecting their warren.
The idea of faith is also destroyed in this episode, as since the Black Rabbit came down and acted, he is therefore objectively and scientifically real - it's no longer a matter of belief, faith, or struggling rabbits trying to explain the tragedy of their existence. The writers, with this move, declared that the rabbit's faith is real, that the black rabbit is real, and that there is a right and a wrong in life. What does that mean for the rest of the universe? The other animals, surely they have their own religions, does this invalidate their religions? What about human religion for the humans in the series? Is the rabbit's gods the only gods?
Oh, and what about the rest of Woundwart's army? Poor, innocent rabbits who are just following orders? Fed lies about a prophecy since birth? Perhaps they're scared that if they don't fight, Woundwart will kill them! Are all of the rabbits that were sucked into the sky truly guilty and deserving of whatever punishment awaits them?
The Magic created a lot of questions, which for me have festered into plot holes, burning through the fabric of a literary universe. Plus, Silverweed was neat, shame he died/lost his youth.