There was not much the Town of East Hampton could do other than reluctantly say yes when a Showtime television production company recently sought a permit for a week or so of taping for episodes of “The Affair” at the end of the month. This is despite conditions that many residents described as intolerable when the series’ pilot was filmed in Beach Hampton in September. Back for more, the company is to tape scenes in five locations in Montauk and at the Lobster Roll restaurant on Napeague through June 4.