Kristin,
Being a first time mom can be one of the toughest jobs there is. We've all been there.
In a "Normal" situation, I would say that you are probably doing everything correctly. Sometimes babies just cry, and no matter how hard we try to calm and soote them, we just have to set them in the crib, or playpen and take a breather. There's nothing wroing with that.
What I'm curious about is the fact that this started after her surgery. IS she still on any medication for pain, or anitbiotics, or anything? SOmetimes babies and small children (And even adults) react oddly when they're on medication. Also, I know you said you don't think she's in any pain, but she may be extremely uncomfortable. After a sergery on a cleft pallet, she's probably getting used to a whole new sensation around her mouth and nose?
I don't know much about your situation, but it couldn't hurt to have her checked out by the pediatrician, ot a surgical follow up...