I would say Mega-Sableye is a good counter.
First off, Mega-Sableye's typing is great for beating Mega-Kangaskhan becaus its movepool is generally limited to Fake Out, Earthquake, Power-Up Punch, Sucker Punch, Crunch, Return, and Double Edge. This shallow movepool means that Mega-Kangaskhan can only hit Mega-Sableye neutrally.
In addition, Sableye gets access to Will-O-Wisp, which can seriously hinder Kangaskhan's power.
Finally, Sableye's great bulk allows it to wear down Mega-Kangaskhan with the damage from burn. It also has access to Recover, which is extremely helpful.
Try to leave Mega-Kangaskhan the last member on the opposing team and make sure that you save Sableye for Kangaskhan.
Because Kangaskhan may have Scrappy before Mega-Evolving, Kangaskhan can attack Sableye with a powerful STAB. I would suggest that you prevent mega-evolving Sableye, so that it still can hit Kangaskhan with a Prankster-boosted Will-O-Wisp.
After you get to burn Kangaskhan, I would suggest mega-evolving Sableye, then spam Recover + Protect + Knock Off (be careful of Sucker Punch though).
The only real threat to Sableye is if Kangaskhan (with Scrappy) tries to set up Power-Up Punch. In that case, try to use a combination of Protect and Recover. Don't use an attacking move because it would be a waste of a turn and Kangaskhan can get a power boost from Power-Up Punch. You can already lower it down with the Burn damage.
Setting up Stealth Rock and Spikes can be an extra precaution if the above scenario happens. It can deal around 37% of Kangaskhan's HP (whenever it switches in) if you set up Spikes three times and Stealth Rock once. Ferrothorn and Skarmory can do this effectively and they can also wall Mega-Kangaskhan (Low Kick may be a problem, however, so I suggest letting Mega-Sableye wall Kangaskhan).
Moveset for Mega-Sableye:
Sableye @ Sablenite
EVs: 248 HP / 252 Def / 8 SpD
- Knock Off / Foul Play
- Protect / Fake Out