We always wear our flip-flops in the showers, and they have always been in pretty good shape at the Rio Grande store. We also only go to BB in the winter and have always gone swimming in the Rio right beside the hot springs to cool off. My little girl and I always have fun jumping from the upstream wall into the water. It is actually pretty deep right there, but with it being summer and summer river flow, no telling how deep the river is now.
Two days is not much at all for a place like BB. I would suggest Cattail falls in the evening. Hike up before sunset, then quietly hike back as it is getting dark, I would bet you will get to see some wild life along with a nice sunset view.
Finally, don't try to do too much. Just sitting and watching the desert is a pleasure most people miss.