No worries! My pool filled about halfway twice (drained once, work continued, more rains, drained again!) It's definitely from the rains. I don't know anything about your ground water levels, but with all the rains ya'll have had this spring, that level could be up and seeping up from the bottom under the pool. With that much water, maybe not. That's ok, too. Your PB put holes deliberately in the bottom of the gunite (will be filled in at plaster time) so if ground water rises, it has a place to go. Otherwise, the ground water could float up (or pop up) your pool.
For the smell, you can toss some jugs of plain WalMart bleach in. I'm not sure how much will be needed to get rid of the smell. Start with 2 and add more as needed. Many people (me included) just leave it for the PB or workers to drain - they see that as their job. A few pool owners hate it so much, they get a pump and pump it out. I didn't because I had too many happy frogs in there, and I'm lazy.
It was a little scary for me at first, but it's all good! Let me know if you have more questions. Others will be along with other thoughts.
Suz