If your daughters ears hurt, she's not going to sleep at night. However, I also disagree with the doctor. With each of our 4 kids, we put them to bed in their cribs, and then if they awoke at night, we brought them to the middle of our bed, and we became the cribsides and went back to sleep.
Of course, this wasn't out of any intentional method of parenting. It was survival. We both had demanding FT jobs, and we needed to sleep. We weren't about to stay up for hours while our child cried in the next room. Unfortunatley, child #4 wasn't a good sleeper -- even in our bed. She'd wake up and want to play with us. (ugh) It was torture at the time, but now that she's 13, we laugh and say, "Wake up, Daddy! It's MORNINGTIME" (in the middle of the night if we both happen to be awake == because that's when she'd launch that at us)
I don't think it adversely affected any of our 4 children to have the security and comfort of being near their protectors during the night. By 2, they were largely in their own beds through the night, and as they got older, they beat a path to our bedroom if they were sick in the night or anything. They didn't have to wait for us to come to them. When they were bigger, if they were sick, I'd give them a sleeping bag and let them sleep on the floor by the bed, so I could get to them quickly, and conveniently, that put them VERY close to the bathroom if they had upset stomachs.
Doctors are trained in pathology, many are very wise, but they are not schooled in parenting any more than you or I. It's all born of experience. Frankly, if your child is anxious about being separated, and it's interfering with your sleep and hers, I'd solve the separation issue, get rid of the anxiety and get some sleep. Separation anxiety is a phase children go through, and it will disappear on its own. But why traumatize your child if it bothers her so much that she can't sleep?
I'd much rather provide the comfort and security she needs now, knowing that with a sense of security behind her, she will have the confidence to tackle the world and win as she grows up.