According to Faction War, characters can no longer be members of Factions that disolved after the War (i.e. Mercykillers, Signers, etc...) But surely some of the members would've held to their beliefs and refused to quit? Couldn't a splinter group restart these Factions (outside of Sigil, to be sure)? And why should PCs lose their Faction abilities if they still believe in them? After all, many of the Factions were started by one person who gained power thru his or her beliefs, before the group was founded, right? And members of Factions that merely disbanded (lost their power structure) like the Dustmen and Ciphers supposedly can't advance in Faction abilities, although they get to keep the ones they already have... I don't like these rules!
Factions disolved/disbanded after Faction War
Here is simple solution for that: you can treat (or reorganise) disbanded factions as sects lead by most loyal folowers of that philosophy. That way you can keep some semblence to faction structure and sense of organisation.
In fact I think it is natural cause of things: they are disbanded, but no one wants to be alone on the planes, so I guess they are bound to come together again as sects, brotherhoods, cults, societis, private social clubs or whatever you wish to call them.
Good example of this is Incantifer sect: they too were major faction in the past but after Lady´s coup they were thougt to be disbanded and destroyed for good, yet they reformed into shape what exist today...
That way you can hawe old factions and their benefits whitout some mayor changes.
As far as Planewalker is concerned on the subject - the factions still have a place in the Planes. Just not necessarily a blatant one in Sigil. (Note: I didn't say they didn't have a place in Sigil still too.) I'm not going to be the one to tell the Harmonium to disband across all of their multiple prime worlds and Arcadia. It just doesn't make *sense* for them, or any of the others, to simply vanish overnight or to withdraw from places outside of the Lady's control.
Rather, Faction War is an expansion of things - the factions took a hard blow straight in the face, they've fallen back but not been defeated, and now their influence is more active outside of Sigil. Influence within Sigil just simply gained an additional layer of intrigue through the guilds, and the entire political situation is in freefall.
The best way to fix the problems you have is to make your own rules. For example, not all of the Godsmen want to join the Mind's Eye? Fine, a group retreat to their former HQ on the Planes and continues on. In fact, Dragon #339 has a bunch of 3.5E rules for former factions (i.e. Godsmen, Mercykillers, Signers). As for the Dustmen and others that disbanded, there's not much you can do because there's no power structure left to train new members in the ways. The PSCS that was written by the good people at Planewalker.com have made all sorts of feats stil open to the faction members, though. Most people, for the most part, seem to ignore the "lose Faction abilities" part and just let factioneers continue to follow their philosophy.