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I hope you have the courage and conviction to stay true to your principles and see them through. Hopefully your startup peers (or at least the CEO) brought you on board for not just your technical expertise, but your leadership and management style.

Being a leader means implementing policies in good faith while trying to tweak them to the specific startup's culture.

Max Schireson (ex-CEO of MongoDB) recently stepped down for precisely this reason. He wrote a great blog post about attempting to manage the balance between work and family responsibilities that you may find helpful.

http://maxschireson.com/2014/08/05/1137/