I think the risks of coffee have been greatly exaggerated, personally. Maybe they have some of those risks in susceptible individuals or in people who drink tons, but there are lots of people who drink a reasonable amount of coffee every day in pregnancy and have no issues. I drank coffee nearly every day with my daughter and she doesn't seem to have any genetic defects and was born at a very average 7 lb 10 oz. Of course, if it makes you feel psychologically better to avoid it, that's your call. But I don't think any of us need to go scaring ourselves about it.
As for caffeine getting into DNA molecules and causing mutations, theoretically it is possible, but we'd have to bear in mind a. the number of caffeine molecules that get to the embryo, b. the odds of a caffeine molecule actually causing a mutation, c. the odds of that mutation actually having any effect on the action of the DNA of the one cell it's in and the daughter cells of that cell--the job of DNA is ultimately to code for proteins, but because of the way the encoding works, many mutations at a single location on DNA don't actually have any effect at all on the resulting protein, and many sections of DNA don't actually code for any protein but are just "filler" so a mutation there wouldn't do anything, d. the odds that said effect is a bad one as opposed to a neutral one or even potentially a positive one (a lot of mutations have an effect something like "change amino acid A to amino acid B in this protein", but that isn't going to necessarily have any impact on what the protein actually does). I don't know the numbers for points a. and b. but I'm not too stressed about points c. and d.
According to Wikipedia, ACOG says 200 mg or less a day is okay.