It's not that all the good guys are vile hypocrites. It's that pretty much everyone the good guys (all two of them, John and Isaac–three if you include the Hale girl) are trying to save are pretty much wastes of space. It's like watching an Eli Roth movie. As bad as they are, you kinda have to root for the witches because the other side isn't offering much to redeem itself.
But hey, second season. Maybe the writers have gotten a better grasp on things.
It looks like this weekend and up to the second season premier (next Sunday), WGN is running a special behind the scenes episode called "Witch War" where they go into all the stuff that they are using to shape the series. Before you give up 12 hours of your life to Netflix, you should check that out. It may spoil season 1 for you, but unless you are a diehard fan of Shane West or Seth Gable, you can afford to have it spoiled.
Like Henry said, Increase Mather's introduction to the show is worth every minute and show be required viewing for every witch hunter player and GM. (Hmmm...I wonder if YouTube has an excerpt?)
Tom