Yes, sort of, for a few seconds
Since OP specifically mentions destroying the atmosphere, in "A Matter of Time" the Enterprise effectively ignites the atmosphere of Penthara IV to remove volcanic ash engulfing the planet and then "harmlessly discharging it into space like a lightning rod".
PICARD: The good news.
DATA: The motion of the dust has created a great deal of electrostatic energy
in the upper atmosphere. With a modified phaser blast, we could create a shock
front that would encircle the planet and ionise the particles.
PICARD: That would be like striking a spark in a gas-filled room.
DATA: With one exception, sir. The particles would be converted into a high
energy plasma which our shields could absorb and then re-direct harmlessly into
PICARD: Turn the Enterprise into a lightning rod?
DATA: Precisely, sir.
PICARD: And the bad news?
DATA: If our phaser discharge is off by as little as point zero six terawatts,
it would cause a cascading exothermal inversion.
DATA: We would completely burn off the planet's atmosphere.
Now, technically the atmosphere was not destroyed, but tension is intentionally heightened over the risk of completely destroying the atmosphere and there is an intentional beat after the planet is engulfed in red before the healthy blue glow ensues.
So let's call that a temporary destruction of the planet (at least in the eyes of the audience).