Is it a good idea to let my baby cry? She has been fed, changed, but cries whenever we lay her down.

Smart baby. For nine months she was close to yo, warm, and protected. Now the outside world is different. Babies love being close to mom. As a newborn it is ok to hold her a lot. It is also ok to let her cry for short periods to "vent". If she has reflux then when you lay her down she will be uncomfortable. Try elevating the head of her crib 45 degrees and see if that helps. You can try a sling to carry her 2.