You really can't. Not without a bunch of zon file editing on the ships, if that's what the trouble is.
Of course, maybe the game got munged. Have you Saved, exited and come back in and load the Save, then still had the explosions consistently do that? Do you have mod soup maybe? If you did a JSGME snapshot of your game prior to activating any mods, you could use that to see if the base game is OK after de-activating the mods, then put them back in and try the game again.
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