I'll take a shot at this with the disclaimer that I'm not a trained professional and that some of the decisions involved here could lead to life threatening circumstances that anyone reading this needs to take personal responsibility for. Also, criticism and comments are welcome, I've written this to try and help, but it is just as true that writing something out and having it criticised makes plain any gaps in ones knowledge.
Looking at how long this post turned out, I've come back to the beginning to add that if your boat had no corrosion problems before, the simplest solution is to choose a new single point to "ground" your negative bus. This might be easiest done by using a metal through-hull, but in that case I would also use the motor disconnect mentioned at the end of the post.
The word ground is a bit abused in recreational marine quarters. It tends to be used to describe both electrically connecting the negative bus to seawater (which should only be done at one point, usually the engine), and it is also used to describe the AC ground which is usually necessary if you have shorepower. Although both of these are often the same physical connection (a single point on the engine), they actually serve different purposes. The AC ground is as you would normally expect in a house, it provides a safe path to ground for dangerous AC current should a fault arise in a live conductor. The DC "ground" can also serve this purpose, should a live AC wire come into contact with a DC wire, but it also has the purpose of providing a low resistance path that a DC fault can travel so as to minimize corrosion. Without it, if you had two faults in your DC ground wire, lets say one to a seacock near the bow and another to the engine shaft, they are unlikely to be at the exact same voltage because or resistance in the wiring. This voltage difference is very much like you took a very low voltage battery, perhaps a fraction of a volt to a volt, attached the positive to the motor and the negative to the forward seacock. The result will be electrolysis, and can lead to erosion of metal. If you look at a galvanic table, zinc has a value of about -1, while 316 stainless is about 0. So, you can actually make the stainless dissolve rather than the zinc if you apply a voltage of greater than one volt and overcome the protection provided by the zinc.
As for solutions, lets start with safety first. If you have an AC shorepower connection, you really need an AC ground or an isolation transformer. The main reason for this is if you have AC and don't connect the ground, then a fault means you could leak current into the surrounding water. Particularly in freshwater, if a swimmer (or hull cleaner) is in the water they can offer a path of less resistance than the water and die of electrocution. Even in "saltwater" the places where we moor our boats are often brackish or even have a freshwater lens floating on the surface so that it could be dangerous for swimmers. An isolation transformer gets around this by breaking the connection with the shore, in it there are two parallel but isolated coils of wire, the magnetic field from one coil creates electric current in the second coil and there is no physical connection with the shore. Thus if a fault exist, it doesn't try to go back to the shore ground because there is now no connection to it. Swimmers are safe. Follow the instructions that come with the isolation transformer to keep people on the boat safe from AC faults.
There may be a third solution, perhaps some of the European members could comment on. I think the use of ground fault interrupts are more common there on dock pedestals and in boats. This could also provide protection, but I don't know enough to say any more.
For the DC side, you can have a completely floating (no connection to "ground") negative bus if you like. However, this requires a great deal of care. You must have no faults in your wiring. Neither positive nor negative wires may contact any metallic bits of the boat. This may be harder than you think, lots of electronics ground the negative to the case, a mast-top antenna might have its mount connected to DC neg, etc.... Because we have an aluminum hull we've gone to the trouble of installing a floating DC ground. However, the first thing I installed was a tester that can be used with a push of a button to check that there is no connection at all to the hull. Every time new equipment goes in, I have to check that we've maintained isolation. Even something like corrosion on a connector might lead to a high resistance fault. Chasing these faults is really difficult if you have typical DC breakers that only break the positive lead in the circuit. We went to the trouble to install double pole breakers that interrupt both the positive and negative branch of every circuit. This makes hunting down faults much easier. With a metal hull, our case is more difficult to isolate completely then if you have a wood or fiberglass hull.
If your boat has a simple wiring system, a floating DC system might be possible. I would disconnect the battery and all the known grounds and then use a multimeter set to the resistance or continuity setting to test to see if any unknown leaks exist. Test between the Negative bus and every bit of metal on the hull, same for the positive bus. If there are no leaks a floating DC system is possible. Because internal combustion motors are so difficult to fully isolate (due to using the block as a DC negative ground) and keep isolated, we have an isolation switch for the motor. The one we chose is double pole again, so that when it is off both the negative and positive are disconnected from the motor. You could do the same if you like and then the path for corrosion to the shaft is disconnected except for the relatively small percent of time you run the motor. This is also nice to have if you want to work on the motor and make sure it is not energized, and if placed discretely is a pretty good anti-theft mechanism. In this case, you should have a zinc on the prop or the shaft, especially if you have something like a stainless shaft and a bronze prop.