For NPC/NPC stuff, you want to use CHAIN, and that can flow back into a state that has PC replies when the time is right.
As for the PC choosing sides, you should set a global variable when they choose a specific response:
PC 1) Yo dood, I totally agree with Haery, here. DO ~SetGlobal("Argument","GLOBAL",1)~
PC 2) Hmm, I'd have to say my vote goes with whoever, on this one. DO ~SetGlobal("Argument","GLOBAL",2)~
PC 3) What, me? Oh no, I'm staying out of this!
Or if the implications of the PC's choices don't matter beyond the conversation, just have one reply link to a state where Haer'dalis/Anti-Haer either expresses indignance, or accepts the praise, or whatever.
Also, since this placed in her J dialogue file (because these conversations are PC initiated like in romances) does everything for the other NPCs still need to be appended to their B instead of J file? Does it make a difference?
Doesn't matter, necessarily, but personally I try to keep "J" conversations in all "J" dialogue files, and banters/lovetalks in "B" files.