It really has to be run that way. Too many elites and solos have powers that say "make a melee basic attack against two different targets." They could have just as easily written the attack as "close burst one, target: two creatures in burst." Those two wordings should not function as differently as they do by RAW, so I just play that they don't work differently.
And unfortunately for those elites and solos, they suffer the mark penalty for the attacks that don't include the person who marked them.
The rules seem pretty clear to me, however people may dislike them. Pg 277 of the PHB has the marked condition described as "You take a –2 penalty to attack rolls for any attack that doesn’t target the creature that marked you."
For what consitutes an attack, refer to pages 269 onwards where you can find helpful information such as:
* "A melee attack against multiple enemies consists of separate attacks, each with its own attack roll and damage roll." - pg 270
* "A ranged attack against multiple enemies consists of separate attacks, each with its own attack roll and damage roll." - pg 270
Which states that the twin strike attack (for example) is actually two seperate attacks, and as marks are resolved per attack, they are subject to the condition on any of these attacks that don't target the person that marked them.