Hopefully you read (or at least glanced) through parts 1 and 2 that talk about how the min-max algorithm can be used to simulate an AI opponent. This article describes some of the problems when using min-max.
In theory min-max can only be used for games that don't have any "hidden information" and in Magic, the cards in your hand and deck are "hidden information". I have no problem with the idea of allowing the min-max algorithm to see all of the cards in you hand and deck. The only possible "problem" that I see is that this might create an AI that is "too good". I seriously doubt this situation would occur because of the complexities of the actual programming.
(Programming is very hard in case you forgot, ha, but you probably didn't forget because you might be a programmer yourself. Programmers have to interface directly with the computer, so technically, programmers aren't human.)
In order to use the min-max algorithm you have to be able to generate all possible moves for both players. I could have also said, "In order to use the min-max algorithm you have to generate all possible game states." I didn't use the term "game state" because I didn't want people to geek out and quit reading my blog. :--)
On a side note, according to Wikipedia there is a variation of min-max that can use probabilities. You could use probabilities instead of taking my suggestion of revealing the hidden information; there is a 20% probability that your opponent is holding Wrath of God in his hand.