There are two reasons.
The "real" reason is that Leene's kidnapping served as a plot device to introduce the gamer to the so-called villain, Magus. In addition, the kidnapping allowed for a neat introductory mission which, despite being flawed from a...temporal mechanics...point of view, was innovative and, better yet, introduced the player to one of the greatest game characters ever: me! (Frog.)
The "compulsively overanalytical" reason for Magus's kidnapping Leene was, as you suggested, to disorient Guardia's forces. We know that this plan was successful, at least insofar as the guard captain and his men had to deal with an enraged king who, understandably, was focusing chiefly on his missing wife and not on battle tactics.
~ Sir Frog
Edit: Sincere apologies for the borderline run-on sentences.