The explosion that hurled the Moon across space was magnetic, not atomic in nature
Perhaps it affected the quantum field and caused the Moon to slip between normal and hyperspace at random intervals.
In three episodes of the first season ("Black Sun", "Collision Course" and "The Testament of Arkadia") and possibly a fourth ("War Games"), it's either theorized or shown outright that a "cosmic intelligence" had a hand in the original lunar explosion and the Alphans' later travels.
Not much wild in that idea. David Hirsch of Starlog Magazine proposed the idea of a Mysterious Unknown Force having a part in the survival of Moonbase Alpha way back in 1980, and the idea has been taken up by many fans.
The whole "Moon knocked out of orbit" situation is just a very elaborate hoax