Really, if you're expecting something to come up that can be pacified, you could just stand there and not do anything for the second or two before the cast starts. Also, using Shield Swipe doesn't interrupt a combo, nor does Haymaker, Inner Beast, Steel Cyclone, or Flash. You could hit Savage Blade, pacify something, then go right back into Rage of Halone.

Considering that almost everything endgame is resistant to just about every status effect (except Ifrit HM - and while we're on that, Pacification DOES interrupt Eruption - you will see the cast finish, but the attack won't actually go off, try it for yourself next time), the only way the devs could fix it is to make some bosses not resistant to everything, which could possibly cause people to take PLDs over WARs for certain content if that pacification gives a significant advantage.