I've just reread the charge action, the Wrathful Descent ability and the Preternatural Speed and Lightning Attack talents a few times, and interpret it really RAW.
From Charge: " The character rushes at his target and delivers a single melee attack. "
From Preternatural Speed: " In addition, the character may use the Swift Attack and Lightning Attack Talents during a Charge. "
From Lightning Attack: " As a Full Action, the character may make three melee attacks on his turn. "
From Wrathful Descent: " When making a Charge against a Horde, the Assault Marine may inflict an additional 1d10 damage to the Horde’s Magnitude after a successful melee attack. "
All of this would mean, during a charge you can use Lightning Attack due to Preternatural Attack for 3 (or 4, if you count the offhand weapon) attacks which all, by the wording, count as a "melee attack" - which is what triggers the +1d10 magnitude damage during a charge. So you can see the dilemma.
I've seen others on the forum count it as just the one +1d10 after the whole charge action has been processed, no matter how many melee attacks you get during the charge - which, to be frank, is the most "non-broken" way to look at it - but it's not really by the wording of the rules.
Another case of badly written rules, or just the most efficient (and broken) horde killer ever? Add in Whirlwind of Death by the way.
Edit: Oh, and I just remembered Thunder Charge. You get 1d5+1 unarmed melee attacks from that one during a charge. I'd assume Wrathful Descent technically should work on that too? Just seems strange, but oh well. I guess that 100+ magnitude horde just died.