Not to worry. A hundred years from now, they'll tear up the pavement and find the Roman town again.
In some ways that is not such a bad thing. As a former archaeologist, it pains me to see sites excavated in the early 1900s and know that they destroyed a whole lot of information that *today* we could have retrieved. In 100 or 200 years, who knows what they could retrieve?
So long as the parking lot doesn't negatively impact the site, I don't really see the problem.