Hey, this reminds me of the time I made the ESB Luke vs. Magnaguard thread!
http://www.killermovies.com/forums/showthread.php?s=&threadid=379829&highlight=esb+luke+vs+magnaguard
But seriously, Luke pwns, anyone who even stands a chance against Vader, conflicted or not, could beat a Magnaguard, and Luke beat Vader, who, even when conflicted, is still far stronger than one Magnaguard.
Magna guards has some missile launching weapon in BF 2, it's really good. Luke coulden't parry it with a lightsaber since it would blow up, but he could probably push it back. But really, the only reason they got that weapon is because they woulden't stand a chance against jedi's or any other unit if they had melee.
Luke wins ONLY because he can use the Force, and even with the Force I'm hard pressed to give this fight to him.
He just does not have the saber skill to beat a magna-guard. In a saber (vs. staff) fight he loses 65-70% of the time. Only with the Force could he win this battle.
I give it to Luke, but just barely.