Short answer:
Yes
Explanation:
Here is Pallando the Soul-keeper’s text:
And here are the rules concerning body checks made during CvCC:Unique. Maia. Manifestation of Pallando. Two strikes. Detainment and -3 prowess against hero companies. Discard this card if Pallando comes into play. As a creature, may also be played keyed to Lindon, Númeriador, Arthedain, or Cardolan; or at sites in these regions. As a permanent-event, the next non-Ringwraith minion discarded from play is instead eliminated. Discard when a minion is so eliminated.
Since Pallando the Soul-keeper has a replacement effect that any non-Ringwraith character is eliminated “instead” of being discarded, and since the rules for CvCC don’t make a distinction as to whether the character would be discarded or eliminated normally (just that the character is eliminated), the player making the body check gets the MPs due to the minion character ultimately being eliminated.Body checks for both defending and attacking characters are resolved normally.
If a defending character is eliminated, the attacking player receives “kill” marshalling points as indicated on the character’s card. If an attacking character is eliminated, the defending player receives «kill» marshalling points as indicated on the character’s card.
As a final note, while it is true that hazards that affect “attacks” don’t have any effect on CvCC, Pallando the Souk-keeper’s replacement effect doesn’t affect “attacks” and thus his effect is active during CvCC.