Hi Kelli,
I have 6 EX-1r’s which I use daily in low light situations using auto-focus all of the time. I shoot through two-way mirrors which drastically reduce the amount of light the camera gets. I have no problem achieving a crisp, in-focus picture with no undue effort. I would have to suggest that there is something wrong with that camera. If there is certified Sony dealer in your area I would bring it to them and have them look at it. They should not charge you since it is a warranteed camera but they may ridicule you for buying it from B&H (since everyone charges the same price for a Sony camera).
You should not be unhappy with the focus.