Until this issue is fixed in opencv4tegra, I did a workaround to use higher resolutions from the camera. I use v4l2 ioctls directly to grab the frame from the camera and then use the Mat constructor to load the buffer into an opencv data type (Mat). Then I do the appropriate colorspace conversion to BGR before doing any processing on the buffer.
Mat yuyv_frame = Mat(CAM_HEIGHT,CAM_WIDTH,CV_8UC2,ptr_cam_frame);
cvtColor(yuyv_frame,bgr_frame,COLOR_YUV2BGR_YUY2);
This works fine for me.