I love Faction War
I've only ever read the adventure and never actually gotten to run it, but I love this module. That said, the fact I haven't run the module is not my only caveat:
As Piratecat indicates, this ride throws a major wrench into the Planescape gears. Factions are, I believe, essential to the setting. But so is radical change.
The Lady has messed with the faction arrangement before, about 400 years ago, in The Great Upheavel. Run the module only if you're willing to deal with the fallout of pulling one of the major lynchpins out of the works, and then finding a creative way to put it back in without WotC's help.
Some of the coolest action in the module comes out-of-game, way out. The NPC's dealings with one another and the eventual fate of the antagonist are likely to remain forever dark to the players and their characters.
The factions are at their best and worst in this module. Sigil has never felt richer or more real. The metaplots come to fruition and some big questions get answered, only provoking new questions. I feel like this adventure is the culmination of the Planescape story, and while, in practice, it turned out to be the setting's finale, it works at least as well as the end of a looong prologue to an even better, longer story.
I highly recommend this product. I say run every other published Planescape product you can get your hands on, especially The Great Modron March, Dead Gods, and the aformentioned Harbinger House. Read them all until you've got the order you want to run them in, run them and then run Faction War.
Once you've done all of that, you should have enough of a sense, a feel for, the Planescape twist, that you'll be able to run a wonderful post-faction war Planescape campaign featuring the return of the guilds/factions/sects/??? and a new era for planar travel and the Cage.