I would like to clarify that the wiki literally says the pact commander is a role of players in the story, which makes sense considering anet only writes what they do, not the characters themselves.
With that being said, you can certainly write a good story while also making it friendly to your character's profile. One way to do it is to give them their own story arc, like in personal story, except this one is their turning point which determines their new personalities. Either it can be linear or choice based which will narrow down the possibility, giving players choices while also keeping all the branches manageble.
Of course, this means your characters' personality will change and might force you to play certain way, but that's inevitable. At least this will preserve your toons' profiles while giving them some character developments.