I installed the new front springs today, and after I stepped back and looked at my work, I realized that one of the springs is not seated correctly, that is, the end of the coil is not lined up between the 2 holes in the lower control arm. Now, I understand this can creat a problem with the car sitting level, so my question is this: Is it possible to put the spring compressor on, and rotate that spring...without disconnecting the spindle? What do you guys think?

I'd give it a try. It's not to dangerous if you keep both ball joints bolted to the spindle. If it doesn't work, and you have already got the spring compressed, break a ball joint loose and seat it correctly. Be careful, we all know how much damage a wild coil can be.
Roger