Hi bblantonator,
If your FPGA can present to Tegra a compliant CSI stream (to get the FPGA to take the two images and stitch them together for one frame to send to TK1 to look like one source, just like a single camera to us), then it should work, but you would need to handle this on your own. In facts, we did not ever do something like this design on any board, so there would be some risk and effort to make it works; the alternative suggestion is to go with USB cameras of course.
Thanks