I'm not familiar with the autoimmune protocol, but for any other Paleo/ancestral/related(I include whole food LC in that), it should be inconsequential. I've yet to see any evidence that ANY starch is detrimental -- it's the proteins that go with (e.g. gluten) that cause problems for some/many.
If you're concerned, of course if you can find an economical starch-free alternative, by all means go for it. But in the scheme of things I'd save my money if doing so was an expensive venture.