I think Pacification is its own issue. Maybe the healer is in the middle of a cast when your Pacification lands. By the time it's over, your Pacification has 1 second left. A missed Esuna on Pacification usually means it was just bad timing. Yes I know that 5 seconds could mean a lot to you but if I'm doing anything at all except standing around, it will likely get missed. We all know that just standing there is also bad.

I always try to Esuna everything if I can spare the GCD and/or everyone's in good shape, even if I look like a dumbass when it doesn't work. I do feel that's part of a healer's job although I also think it's dumb that other pure casters don't have a dispell!