I've ate here for many years but only a couple of times since being diagnosed two years ago (I live in the east bay now). I have not got sick these few times and I'm extremely sensitive. The food is GREAT! Talk to the manager and maybe don't eat non certified rice etc.
Their menu mainly caters to vegans but you can get some tasty GF items by ordering things with corn tortilla instead of flour. However, if you're looking for a meatier Mexican option you can get something cheaper and just as tasty at other Mission eateries since most serve corn tortillas.