Yes, you can't throttle GPU usage through BOINC, but you can use various GPU utilities to do that (reduce the operating frequencies, power limits, voltages). I use MSI Afterburner for tweaking my GPUs, I wrote about it here (it's about overclocking, but you can downclock just as easily):

https://steemit.com/gridcoin/@vortac/gridcoin-gpu-mining-8-to-the-edge-and-beyond