Hmmph.
Even if I test with Global.getCombatEngine().isEntityInPlay(missile) and Global.getCombatEngine().isPaused(), it's throwing a NPE. It shouldn't be ever, ever trying to spawnShipOrWing() under those circumstances, we're in Refit (kind of surprised that this script is running at all, tbh).
Since this appears to be another goofy AI issue (at least on the surface, based on the log)... I'll set up Cruisers to use my Frigate AI for a moment and see whether that stabilizes it... maybe the Cruiser's AI is going nuts because a fighter has spawned in Refit (even thought that should be impossible).