E.,
My son has gone through variations of this since he was around 2 years old. First, it was night terrors and then as he got older a fear of the dark, and most recenlty being afraid that a 'spooky' is under his chair in his room.
I've read tons of stuff on sleep patterns and anxiety and it's overwhelming and daunting to try to figure HOW to help them get comfortable. So, I've adopted a few attitude changes...wherever my son falls asleep is no big deal (which it sounds like you've already got down) and there is always a creative solution to be found with lots of talking and team work.
When my son became afraid of the dark it was very much like your little girl, he'd either fight going to bed or he'd wake terrified and would force himself to stay up. Taking cues from our kids is so important, but sometimes tough while they are still developing the ability to explain things on their terms. After talking to my son for about a week, I figured out that he wanted me close because the shadows in his room, and MY room too, were spooky. So, I followed my Mom's route she took with my little sister when we were kids. WE as team went to the store, and I explained that we would get nightlights and flashlights to keep the shadows away. We had a party that night with Grandma and Grandpa, and he showed us how/where to put the nightlights and chose the best places for the little flashlights. And, because its fun we can up with a dance and song to keep the spookies away.
This was a nightly thing few a couple weeks before he would go to bed without total hesitation. But, now its one of those things we pull out on nights he's spooked or after he's seen something that has spooked him.
My advice to you is to sit down and talk with your little girl, and ask her why she's afraid for Mommy to leave. Remember seperation anxiety can rear it's head at any age/stage too, so this could be a symptom of just wanting some more Mommy time. It's tough but even when we think we spend tons of time with our kiddos they really can just start to crave one-on-one time with Mommy or Daddy. I see it with my son when he starts to miss me or his Dad, and I do my best to address it and help him work through it.
Once you know what is really bugging her, ask her to help you come up with a plan to help her sleep better at night. Make you little one a part of the solution and give her power over the issue at hand. I use the terms, teamwork and Big Boy(or Girl for your situation) a lot when we hit an obstacle. This makes my son feel like he is doing something on his own and kids this age love ownership of things that make them feel strong and in control.
I hope this helps...really it will get better. Just be creative and be positive, don't let her see you sweat over this. Kids at any age can read our emotions and then mimic them in their own ways.
Good Luck!!