Makala is brilliant. For almost the entirety of the game, the heroes are playing right into his hands. His plan of using the moredhel as a distraction is essentially a win-win scenario, only marginally complicated by Gorath's warning to the prince - either the moredhel invade, and Arutha responds to the invasion by sending his armies north, or he is warned in advance that they plan to invade, and sends his armies north to prevent it. Either way, his army is relocated to the border, leaving Sethanon and the Oracle of Aal unprotected.(Remember that after Gorath and Owyn are captured, they are set free by a mysterious magician and never find out who it was. In retrospect, Makala or one of the Six seem like the obvious culprits.)
When you think about it, it seems all but obvious that Tomas's convenient poisoning by a moredhel arrow is Makala's doing as well. Not only is the timing implausible otherwise, but Makala is one of the few people with the resources to research/create a (magical?) poison that could debilitate a Valheru, and through the Six also be able to equip moredhel archers with it. Not only that, it's known that Pug and Tomas are friends and that Tomas would try to rescue him, and Tomas is the only other person in Midkemia both inclined and powerful enough to mess with Makala's plans,so it's inconceivable that he wouldn't have taken measures against him.
Finally, sending Pug to Timiranya was a very clever decision and he was likely justified in assuming that a rescue would either fail or not happen soon enough. Why? Magic doesn't work there. Someone coming after Pug would have to be able to traverse worlds, i.e. be a powerful magician. Powerful magicians usually do not weigh themselves down with non-magicians when visiting alien worlds. Powerful magicians (and certainly Great Ones) are also seldom experienced in non-magical combat or survival skills. Thus, anyone trying to rescue Pug would be a magician, either alone or with other magicians, and probably wouldn't last long on magic-less Timiranya in the hostile terrain and with hostile natives. So if a rescuer had walked right in, they likely would've died, and if they'd found some way to discover the planet's nature in advance, they would've tried to find some solution for it before going in, which would've taken time. Gorath and Owyn travelling to Timiranya blindly - a warrior and a magician who is not yet too over-reliant on magic - is the first thing they do that really crashes Makala's plans.
Pretty much every tiny mini quest in the game is tied to the main quest by some thin, barely visible thread. For example, the missing gem you learn of in La Mut at the start of the game makes a lot more sense once you find out that the Six are Tsurani Great Ones who would need a gem like that to power the rift in the Dimwood.