It would be just as easy to buy a 1-both-2 position Perko battery switch for $30, and with the same amount of wiring, you could switch between batteries each day...
ex. Run battery #1 all day, then battery #2 the next day.
If battery #1 dies, then just switch to #2 to get home!
If they are both weak, switch to the 'Both' position, this may have enough juice to get the engine started. The 'Both' position parallels the batteries, just as you previously described.
It gives you a spare battery that should be at 100% charge to get the motor running.
The alternator / charger would only charge the battery that was selected... unless you ran it on both for charging, then selected either battery for starting.
Here's a link to one for less than $30... I don't think you can get a decent battery disconnect for much less.