Per my own answer over on Scifi:SE, The screenplay for Matrix Revolutions makes it abundantly clear that the clouds unleashed in 'Operation Dark Storm' are comprised of "molecular replicators" which are totally hostile to the machines. When entering (or even approaching) the cloud layer, the sentinels are instantly "drained of life", then struck by bolts of high-powered lightning.
We can assume that any attempt to dismantle this layer would be a monumentally difficult task. Not only would they be unable to even approach the clouds but since the layer is comprised of "replicators", it seems pretty likely that when you try to destroy them, they ... y'know ... replicate:
Scene 737 : EXT. BLACK SKY - NIGHT
Rocketing towards the churning black sky, leaving a white-hot jet trail that cuts up from the black earth at a forty-five degree angle.
Several Sentinels leap from the back of the ship, but many remain as it barrels towards the dark roiling ceiling.
The Logos plunges into the sky with a surreal splash, like a plane crashing into a sea of shaving cream.
The molecular replicators immediately drain the life from the Sentinels and they fall dead tearing through the clouds that cling to
them momentarily like shredded pieces of parachute, before letting
them fall away.
The Logos is engulfed by a ball of lightning as it is attacked by the sky. It shakes violently, every light blowing out, until the ship