The factions are built into the module to provide very specific rewards and benefits. If you ignore them because of the FR lore, you lose all of that stuff for players. It's integrated into the module. OTOH, if you want to keep the factions and benefits but de-couple it from FR, you have a lot of rewriting to do. This is not that hard to understand.
I had more here, but forget it. I'm done trying to explain things to people who can only hear their own voice.
Carry on!
Uhhhhh no.
All you have to do is change the name and make up your own little lore about it and off ya go.
How long have you been playing D&D? I could understand someone coming in for the first time and having difficulty coming up with their own lore but not someone who has been playing a while.
You can change rewards and anything else that's there. Seems to me the problem is you just don't want to have to do any of the work.
Why would you even want to play or run the module if everything about it is not to your liking because you apparently want to change everything?
Why not just run a homebrew game and make up your own stuff?