Corn tortillas aren't perfect, but passing up good tacos because of a couple of them would be the greater evil. Sure there are better options, like doing a lettuce wrap, rice torts, or turning your tacos into a salad, but that's not what you asked.
If you've had the rest of your diet locked down for a while and can handle a small cheat without spiraling into a week-long binge, I say eff the Paleonazis and enjoy your corn tort tacos with a NorCal margarita.
A TORTILLA KILLED MY DOG WHILE WORSHIPPING SATAN. EVIL.
But seriously, flour ones are bad gluten juju and should absolutely be avoided. Corn tortillas are not good for you, but are not a horrible, horrible "cheat" (though nasty, rancid oil-fried tortilla chips are a bad idea, no matter how delicious). If you can get traditionally fermented corn tortillas (you will probably have to make these yourself unless you live in Chiapas, etc. or hang out with persons of indigenous Mesoamerican descent), those are OK by me. Some people make coconut "tortillas" which I haven't tried and which sound weird.
In summary: flour = chaotic evil; corn = neutral evil; fermented corn = chaotic good?; coconut = unknown, possible lawful good
The traditional preparation of corn before cooking is soaking in an alkaline solution, this is called nixtamalization which frees up the niacin in the corn. Nixtamalized cornmeal is called masa. When Europeans began growing corn as a staple food without this, they developed the terrible deficiency disease pellagra. Of course, pellagra is only a problem if you base most of your diet off corn.
Evil? No. But I don't use such words for any food. There could be evil people involved in production of any food, but I don't think you could say corn is evil, unless it's been spliced with octopus DNA, then it is an abomination....
I was in a Mexican restaurant this weekend. We consciously try to be Paleo and Gluten free, but I do allow the kids non glutinous grains. I ordered corn tortillas for their meal, as I usually do, and I told the waitress that we were avoiding Gluten. Out ran the chef and said that all tortillas, including corn, had flour in them as a binder. Wondering how many other mexican restaurants do this?
Most corn is GMO, so maybe better to avoid it all anyway.
I would avoid both. These, however, taste awesome and are totally paleo: http://paleograd.blogspot.com/2011/02/paleo-corn-tortillas.html
real tortillas are made with lard, water, flour (corn or wheat). They are super easy to make at home, and millions of people make them daily.
I would go for corn ones, myself, and use home-grown corn, preferably sprouted. I can make a batch of 2 dozen in about 20 minutes.
Wheat-Flour tortillas are awful for your health, even worse than bread because typically their oil is horrible. Corn tortilla are not good either but if they are made with a decent oil they may not be that bad, perhaps just a little worse than having white rice.