Restricting yourself to only Gen 1 Pokémon is a bad idea (Golduck? Really?).
Fortunately for you, there is a Gen 1 Pokémon that is a fantastic counter to Mega Kangaskhan: Gengar.
-Gengar, Killer of Khans:
Nature: Timid
Item: Black Sludge/Life Orb
Ability: Levitate
EVs: 252 Sp.Attack, 252 Speed, 4 HP
Moves: Shadow Ball, Focus Blast, Will-o-Wisp, Substitute
Thanks to its Ghost type and Levitate, Gengar is immune to Earthquake, Power-up punch, and Normal attacks. Sucker Punch won't work when it switches in since Sucker punch requires that the opponent needs to use an attack move to work. Your opponent will probably think you're some idiot, using Gengar when their Mega Kangaskhan has Sucker Punch. That's where they're wrong. You first use Will-o-Wisp to burn the Khan; Gengar will be safe because Will-o-Wisp isn't an attacking move. On the next turn, you use Substitute to give Gengar a temporary shield. It is safe once again because Sucker Punch doesn't work when you use Substitute. Due to the last 2 turns of burn damage and the Substitute, Gengar will survive the Sucker Punch, and KO Mega Kangaskhan in one shot with Focus Blast (provided it doesn't miss).
So whaddya think of that? The nice part is that Gengar is a generally good Pokémon.
Outside of Gen 1, you could use Conkeldurr. It has pretty good HP and Defense, and great Attack. It resists Sucker Punch, and has the HP (especially if you put EVs into it) and Defense to stomach Mega-Khan's attacks, then smash it with a Fighting type attack, preferably Drain Punch (you have to breed it with a Meinshao to get the move).