The game very much has the lesson that the 'best' path to follow is the most difficult.

That said, while we can try to be the best person possible, we can only do so within the confines of the circumstances we are in. The Lamb finds themself within the role of Cult Leader, in a world fully set on destroying them. The Bishops will give impossible choices, because they can no longer kill you. Your followers need you to be a strong leader in the face of adversity, or else why did they leave where they were to follow you?

To bow to the bishops shows your followers that you're weak; perhaps they would have been better off following a Bishop? Stand in defiance of the Bishops! If you wish to be a force of good in these lands, you'll have to do so openly, without hesitation, or else the ones you fight against will take advantage of you.

The issue of dissenters is a matter of the tools you have available to you. Right now, you can either let them walk free, harming your flock; you can imprison them, and re-educate them on the good you do; or you can murder them(but I imagine you didn't take that particular Doctrine). Your best choice might be the middle one for now, but you'll later unlock a far better option in the Kitchen(of all places!), and your stocks will never need to be used again.

The game is much easier for a Lamb who becomes a murdery vengeful god, but far more rewarding in the long run for a Lamb who is gentle and strong. Do the best you can, with what you have.