To me, this is different in each relationship. And one thing, I think, that made it easier on Karma was to know these boundaries would eventually change.
Currently our boundaries follow our rule of "Happy, healthy and sane," for all parties involved. In the beginning, the boundaries were tight because Karma and Cricket were both trying to rebuild trust with me. I needed to know I could trust them, individually and as a couple. So the boundaries, or rules, as we called them, were tight-- no seeing each other without me there, physical contact was limited, phone calls and e-mails were subject to me being there. No hiding. To me, they lost the right to privacy when they had the affair. As the trust grew, I pulled back on a LOT of that. They were allowed to drive her home without me there, they were allowed to go to a friend's house without me, I stopped reading every e-mail, I encouraged physical contact, even sleepovers (though I had a hard time with that, as I pushed it a little too soon). And we instituted the 24 hour rule-- as long as I had 24 hours notice, they could have visits without me. Eventually it became only about respect and safety.
Our boundaries now include honesty, respect (do I have plans? am I feeling okay? and me respecting them and their plans), and safety. Happy, healthy, sane, as we call it. As long as we are all happy, healthy and sane, it's okay. If not, then it's required we sit down and find out what the issue is and how to fix it.
So, after that long explanation of where we are, my question is, what boundaries are you setting that she feels are getting in the way of who she is?
As was said by someone else, if they are your NEEDS, then they need to be respected, but you also need to respect hers.
Compromise is a huge part of making this work. I believe in compromise, not sacrifice. I think if compromise and communication are an issue, it's time to analyze your relationship, as it stands.
Karma and I are far from perfect, but communication and respect of each other's thoughts and feelings have made all the difference in making this work.