Heaven was a mythological paradise in many cultures. The term could also by synonymous with the sky.
In 1996, when Porter observed Lieutenant Tuvok using a phaser, he believed it to be a laser and commented "God in Heaven help us," but The Doctor replied that divine intervention was unlikely. (VOY: "Future's End, Part II")
In the 22nd century, Kai Taluno of Bajor claimed his ship was "almost swallowed by the heavens" near the Denorios belt. In fact, he had witnessed the opening of the Bajoran wormhole. (DS9: "Emissary")
In 2366, Geordi La Forge stated that he hoped the non-corporeal Koinonians invading the ship's systems wouldn't "blow us to Kingdom Come while (they're) figuring out how to blow us to Kingdom Come." (TNG: "The Bonding")