Adding an isolator is just something else to go wrong. Its a fix where there is no problem. There is no reason for it unless you are pulling juice while the motor isnt running, and want to keep one batt charged for starting.
Another thing to consider if you plan on removing one batt is that you will wear the brushes in the starter faster. Using one battery means less volts to the starter under a load, which means its going to pull more current to use get the same power. This definitely will case the starter brushes to wear faster.
This is usually seen when people replace their automotive style batts with deep cycles. Deepcycles run at a lower voltage, and are a bit harder on starters.
Its not going to immediately kill your starter, but will take life off of it. Maybe 20% - something like that. I still like the deepcycles though, and dont mind replacing the brushes.
If youre not in a cold climate, you probably wont miss the second batt, but it will turn over slower on starts.
If you want, disconnect the ground on the second battery so you can test it for awhile without the current from that batt. Its a safe way to take it off-line to see how it works without it.