It appears that Mr. Epstein did, in fact, name Mr. Felt in his original Commentary article. The relevant passage is below (via Powerline):
Bernstein and Woodward identify their main source only under the titillating code-name of “Deep Throat,” and indicate that “Deep Throat” confirmed their suspicion that Segretti—and political spying—were at the root of the Watergate conspiracy. But who was “Deep Throat” and what was his motivation for disclosing information to Woodward and Bernstein? The prosecutors at the Department of Justice now believe that the mysterious source was probably Mark W. Felt, Jr., who was then a deputy associate director of the FBI, because one statement the reporters attribute to “Deep Throat” could only have been made by Felt. (I personally suspect that in the best traditions of the New Journalism, “Deep Throat” is a composite character.) Whether or not the prosecutors are correct, it is clear that the arduous and time-consuming investigation by Woodward and Bernstein of Segretti was heavily based on FBI “302” reports, which must ultimately have been made available by someone in the FBI.