Basically Zenning, based on the rules of time travel we view later on in the series, Marle shouldn't have dissappeared.
I always kind of thought of the Chancellor as being the Mystic's "inside agent" (basically their spy) and that he basically did w/e he could from within the castle, including the capture of the Queen...So, while it could have been a direct command from Magus (or one of his generals), I think that it's possible that Yakra acted on his own...or maybe Yakra was another of Magus' generals...or w/e's under 'general'?