The Aura allows the beholder to make an attack, and this attack would indeed suffer the relevant penalties.
The second part of the question is debatable. My interpretation is that the only attacks that can include multiple targets are attacks such as bursts and blasts, and attacks that target X creatures (where X > 1). So a ranger using Dire Wolverine Strike or Split The Tree that includes a target which marked him, would not suffer penalties, but if he uses Twin Strike, any attack that doesn't include the marking enemy would suffer the penalty.
If an attack has a primary target and secondary target such as with Force Orb, the primary target must be the marking enemy. Otherwise the attack will suffer the penalty.
In the case of a power like Lightning Bolt, if you were marked by enemy A, but attacked enemy B as the primary target with the Lightning Bolt, you would suffer the penalty on the initial attack. But if one of your two secondary targets was enemy A, then your secondary attacks would not suffer the penalty.
Here is the generalization: Any (primary or secondary) attack that forces you to choose targets before the attack rolls, will not suffer penalties if you include the marking enemy. Any multiple attack power that allows you to make target decissions during the attacks, will cause you to suffer the penalties for any attack that does not target the marking enemy.
Clear as mud?