[Considering that when the LIRR stations were open the ridership could have been counted on the fingers of both hands I doubt such a line would be profitable at all. Are the buses going through those areas packed like sardines??]
While I agree that a subway conversion of the Lower Montauk wouldn't be a wise idea, the LIRR's lack of success is not one of the reasons why I think that way. LIRR service was nearly useless for decades at least. Except for Richmond Hill and Glendale, the stations (if you can call them that) were in middle-of-nowhere locations and service was minimal. Subway transfers at Long Island City required a fairly lengthy walk to the 7 at Vernon-Jackson, only to squeeze onto grossly overcrowded cars.