FULL GUIDE FOR ANYONE LOOKING THIS UP IN 2017
You basically need to repartition the disk to GUID, but because your system is on it, you can't do it with disk utility (the option appears greyed out). We will make this work by doing it in recovery and reinstalling a backup.
So here are the steps:
1. Make a time machine backup on an external drive
2. Power off your macbook
3. Power it on and press cmd+R while it is booting up to boot it into recovery
4. After recovery loaded, go to disk utilities
5. This time you can repartition your drive: click on your drive and erase, in the option select GUID partitioning. (THIS WILL ERASE EVERYTHING FROM THE DRIVE)
6. After that is done, still in recovery, choose to restore your data with time machine.
7. After the restore, your macbook should be just as it was before.
8. You can now update your macbook to OS Sierra without a problem.