After defeating Logan can you be “all good” and win

Yes.

They increase in number as you progress through the game, and unfortunately there isn't really any way to stop them. It doesn't really have to do with your decisions, but how far along in the game you are. I have yet to discover any pattern to their arrivals (I have seen them during the day) so I'm not sure there is any way to avoid them unfortunately. Note that they only appear "in Silverpines, Millfields, Mistpeak Valley and Hero of Bowerstone's Tomb".

As far as defeating them, there are a few weapons that provide bonuses against balverines. They are:

• Lunarium Pounder (Hammer): +40% damage after killing 100 wolves or balverines
• Trollblight (Hammer): +80% damage (they count as large enemies) after killing 10 large enemies with a flourish
• Wolfsbane (Sword) (Limited Edition Only): +40% damage after killing 50 enemies with flourishes

I believe they may also count as evil enemies (couldn't find a place that said for sure) so if that is true, any weapon with bonuses against evil enemies will count for them as well.

Other than that, I'm not sure if there is any real 'good' way to beat them overall. It would depend on what skills you have so far, how many there are, what weapons you have, etc. If I remember correctly, by the time I was maxed out on everything, I think balverines were fairly 'easy' (though enemies level with you so it will only ever be so easy).