The drag caused by having a fixed prop in the water will be quite small.  There is some debate about "windmilling" online, but lots of sailboats have fixed props.  Long shaft outboards have only become common quite recently.  If you buy an old yacht with a motor, chances are the prop is in the water all the time.

The other thing to remember about boats is that any design has a "hull speed", and below this speed the boat can easily move through the water, but once you exceed it the drag forces go way up.  Once hull speed is reached, it is very hard to get a boat to go any faster.  Dinghies will lift out of the water, but a yacht is ballasted differently, and normally the keel stays in the wet stuff.

By measuring the speed of the windmilling prop, it should be possible to determine when hull speed is reached, and apply regeneration at this point.  Yes, once it is regenerating it is going to produce some drag, but since hull speed has already been reached, the drag is likely to be irrelevent, reducing speed by only a few percent.  Below hull speed the regeneration electronics should detect the prop RPM and electrically disconnect the motor/generator to save drag.

A boat that has a hull speed of 3m/s (6 kts) should be able to generate about 3 1/2 kW at the Betz limit from a 15" prop (water is much more dense than air).  But if your boat is carrying (say) 24kWh of storage - enough to provide plenty of ballast, and to run a 6kW motor for 4 hours/24 nautical miles - then you might want to generate only 1kW to recharge the batteries.  That gives you 24 hours at hull speed to recharge the whole bank ready for arrival in port.  The drag represented by 1kW at 3m/s is 333N - about 75lbs of drag.  But in a stiff wind you're never going to notice that.

Poking around on the Internet shows that this is not just theory.  Solomon Technologies are already fitting electric motors with regeneration to yachts.

http://sailingwaypoint.com/
http://www.catamaranco.com/electricLagoon/faq.htm

I still think I'd use a 24v system, so the auxiliaries could be run from the traction battery, and the PV panel/windmill setup could keep the traction battery "topped up".

But that's details.  The main point is that the system works.

The largest motor EVAmerica sells for a CAR (for highway use) is 30hp!!  And that's to propel a 2,000lb vehicle and a 1,000lbs of batteries down the freeway at 60mph!!

I'm thinking a 5hp DC motor would FAR outstrip the original 10hp Deisel for performance.