Is there any way to make someone like them?
It could have been a very interesting faction. Yes, they were fanatics, but most of the people in the Outer Planes are. But someone seems to have been carried away when writing about them. Currently I know no person who could even like them, less alone play them without turning them into caricatures of themselves.
Sarin's reign seems like a joke. It was a series of failures and PR disasters. Death... err... training camps on Nemausus. Indep hunting games behind his back. Fortitude and its unfortunate "ascension". Maybe he was just incompetent, but even reading about Ortho is disturbing. Extermination of elves and pixies?
Do you have any ways to make them less one-dimensional and eeeeeevil before the Faction War? Something that would make them seem even likeable in the eyes of more lawful oriented players? Ore are they a lost cause and nothing short of a radical change (as in 3.0e stuff) can help them?
I think the Harmonium is indeed the exact opposite to one-dimensional. It's intentions are the best. It offers order and safety and gives everyone the chance to be part of and to help to shape a secure and better world.
But then there are scumbags amongst its members who don't get what the Harmonium's about and abuse it's goals and the power it gives to them to force others to their way of life, but don't get caught, because they're basically playing by the rules.
The Harmonium is great, because it is ambivalent, or hat an ambivalent side, at least, unlike many other 'good' organisations.And a leader having no absolute control over his organisation and no total insight in every action of its members is definitely more realistic then the opposite, especially when you're talking about such a vast organisation as the Harmonium.
I think it offers lots of options to the DM. You can use the Harmonium as ally, or adversary to your PCs - or even both. Your Harmonium characters can try reveal the nuisances, or decide that it's best for the greater good to let them happen, or even participate in them.
"La la la, I'm a girl, I'm a pretty little girl!"
--Bel the Pit Fiend, Lord of the First (in a quiet hour of privacy)