Aaron,
the APIs Ashish was cautioning you about directly interact directly with SYS/BIOS's interrupt controller management; hence you should use the Hwi APIs to avoid unpredicted behaviors.
SYS/BIOS doesn't have a direct API to communicate with I2C. TI-RTOS 1.21 has a I2C driver, however not for the I2C controller on the AM335x. I would encourage you to examine the I2C driver's code, as it uses TivaWare APIs to access the peripheral registers (which follows StarterWare's model). While the API signatures (and the peripheral) between TivaWare and StarterWare may differ, you can still examine on how the ISRs and RTOS primitives are implemented and utilized. I think this might save you some headaches in the long run.