That's the intended effect of PLD by design. It's how PLD plays in CC as well. Cover is meant to take all CC to the PLD. Otherwise, why would you pick PLD when it just has the lowest DPS of all the tanks?

That being said, you can still easily counter them with CC or even NIN LB. After all, they have little to no damage at all. Just bully them after they capture the flag and make their points gained useless. They can't contest against anyone if they're always beaten up and your team gets Battle High faster. Battle High is what ends up winning the game in the end.

It's pretty much a skill issue at that point if you keep on getting beaten up by the PLD cheese and can't win objectives. PLD cheese is really easy to beat as long as you have team members that hard focus them once you identify who they are. The main key point is that you can't let them play to their strengths (AKA let them freely capture and then run away without penalty). You either have to attack them early to break their plan ahead of time or punish them for using cover and guard early so that they have to die and respawn while your team gets higher stats from Battle High.