It should probably have at least some effect on morale, unless there are other colonies in the system (under the assumption that the colonists would be given a chance to use in-system transport to reach those).
Otherwise, it's abuseable. After getting very VERY few colonization events (1.05.71) even on a huge map, I systematically pumped out 1M-pop colony ships in systems with empty planets, destroying the colonies immediately, just to get enough events to move morale. I managed to swing to good (very time consuming; basically nothing except taking a 30% PQ hit seemed to move morality very much at all), eventually enough to get all the good techs except Galactic Pacifism, then all the way down to pure evil (seemingly far faster to do, if you get kill-the-worms events and so forth). If the Drengin hadn't figured out how doomed they were and surrendered (ending the game as a Military Conquest), I would have been able to snag all the evil techs as well.
(Another way would be to assign zero or one colonization events to each and every planet at galaxy creation time, then remembering to cancel the event once triggered. Although it might be interesting to allow the event to be asked once for each player who ever controls the system etc. -- e.g. the new owner must decide whether or not to keep sacrificing people to power the Precursor PQ-boosting device. If so, he takes a step towards evil if he hasn't already; if not, he looses the PQ bonus if the previous owner had been sacrificing. That'd require more bookkeeping and a fair bit of work to decide which events were 'recurring', and which could not be undone, e.g. you can't bring the worms back if somebody else killed them all already).
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