I think part of the problem is that in the first run, the Wisdom was the excuse used for the decision that the guy who pulled the switch actually wanted to make anyway (note how insistent the Wisdom is to Kyr that it doesn't decide or act, she is the one doing that) and in the second run it was sufficiently damaged that it didn't have time to run through the options and find a better one... especially since its not-so-secret final goal was to fake its own death, and possibly it felt justified in a bit of selfishness there given what people did with its capabilities.