I still think it would make much more sense to have the old SF station become a terminal for the Lexington Line once the 1 moves to the new terminal, with it as I would do it (as noted previously):
Revival of the old shuttle between Bowling Green (short platform) and South Ferry (using the OUTER platform at South Ferry), most likely using a two-car set of R-62A's.
6 during overnight hours (extended from Brooklyn Bridge).
5 at all other times.
While it may have been deemed "unsafe" to have the 1 train stop there (though the new station was a very well needed piece of work after 9/11 when jobs were leaving lower Manhattan at an alarming rate that will allow for a new transfer between the N/R/W and 1), the station would be far less used (probably 25-40% of what it is for the 1) for a hodgepodge of the old shutte/5/6 depending on the time and day, and for that it would be safe, since ridership would likely be more in line with what that station was intended for in the first place. Since from what I have read it is what many SI Ferry riders want, it is something that should be done.
It also would be good, especially during the late night/overnight hours when women in particular (but not only) in many cases would probably be a lot more comfortable taking the subway to the ferry if they have the option to take either the 5 or 6 (depending on the hour) to SF as they may not necessairly be comfortable walking from BG to SF to get the ferry during those hours.
While I know about the first five cars issue, as long as their are posters in stations reminding people to use the first five cars at South Ferry when the 5/6 would be running there, I suspect there would be minimal problems (and regardless, it would NOT be like the 1 train since it would be during off peak hours since the shuttle would be running when all Lexington service is otherwise going to/coming from Brooklyn and it would also be far fewer people than with the 1 as well).