When you boot up kernel, just add maxcpus=2 in command line, kernel will only boot two CPUs.
Also, you can cut the VDDARM23_IN, and config the menu config to support two cores and rebuild kernel.
These cores are identical, I think for your experiment, you can just add "maxcpus=2" in command line for testing. And for you product, you can get our Dual core version i.MX6D.
Also, you can "echo 0 > /sys/device/system/cpu/cpuX/online" (X is 2 or 3) to remove one core. echo "1" is to add them back.