What you says makes sense.
Your diode idea will work, however like I allready said battery voltage will be reduced, if your charger is a simple device that doesnt measure the voltage then it probably wont make any difference having the diodes.
It becomes more apparent when the engine alternator is charging the battery, it thinks that the battery is at 13.8v because that is what is present on the alty o/p terminals, but the battery(s) will actually be that -0.6v=13.2v (diode forward voltage) , whch for a lead acid is a significant difference, if your boat is used occasionally it'll still probably work well enough, for a house boat though battery life would be significantly reduced, in which case the expense of a charge controller is justified.