Well, the novels have established that there was a lieutenant commander's rank in Earth Starfleet at least after the timeframe of the series. But I see no reason to retcon the existence of one during the series. I mean, when are we ever going to see another story set during the series' timeframe? The novels are far beyond that timeframe now, there are no anthologies in the foreseeable future, and nobody's bothered to get the ENT comics license. It's just not something that's ever going to come up, outside of fanfic.
And I don't see why it's desirable. Why insist that Earth Starfleet do everything
exactly the same way the UFP Starfleet does? Heck, tons of fans have complained about how it wasn't different enough as it was. But one of the differences that the creators clearly intended it to have was a much simpler rank structure. I see no reason to ignore that conscious change.