Dual battery systems do not have to isolated to be effective. If the system you use works, then stick with it. I, too, debated about the best way, and with 30 years experiance in the automotive repair field I know that, for example diesel trucks with a dual battery set up use no relays to seperate the batteries. What they do, that is different, and the way my batteries are connected is very simple. The positive cables to the boat are connected to the positive post of the main battery. The negative cables to the boat are connected to the negative post of the second battery. Then, the batteries are connected together in parallel. This does one very important thing. The batteries are discharged and charged evenly. The biggest enemy in a Marine battery's life, are number of cycles (discharging and recharging) and heat. When you isolate one battery and discharge it completely, it has not only been thru one deep cycle, but also creates more internal heat in the recharge process.
Diesel, I am in no way saying your system is wrong. I decided after my own experiance and research, and a pow wow with my Interstate Battery rep.(who knows batteries inside and out), that this system works the best for me. Even after a day at the beach running 2 amps, I have never had an issue. You are right about one thing, if you poop both batteries, you are screwed, so I just keep a booster pack charged and on board just in case. However, in 3 seasons with my 2002 maristar 210 have never had to use it. The other important thing for a marine battery is to keep it fully charged in the off season. When a battery becomes discharged, the acid absorbs into the plates causing sulfation, and leaves the water in a state that will freeze.