Other games do similar things and it's not the end of the world.
But I think a better solution, personally, is to hold weekly events that involve under-utilized characters. They're sort of doing that now, though it isn't every week, and it's getting me to invest in characters that I normally pass over. That said, I'm not spending money to do so (can't afford it right now! It's not a matter of being opposed to spending or being angry with the game--I'm just at a point where $20 a month is better-invested in higher quality food :P ), so maybe a faction boost would make them more money.
They've got better data on income and what is likely to influence people to spend than we do, so I don't doubt that they've considered a faction boost and decided to go another route.