Indeed, battery depletion is one of the reasons why I prefer (and went with) the Readybrake system over all of the 'electronic box' type systems.
However, there is an easy solution to this, that I highly recommend in many cases regardless of brake system used: Run a (fused) charge line from your MH, through the 'umbilical cord' going to your toad, to your toad's battery. In most cases it is a very easy thing to do, parts to do it can be had for very little $$ (just requires a little wire, connectors, fuses, etc).
This will keep your toad battery charged up whenever you're towing, and you'll never have to worry about the toad battery again. Even if you accidentally leave something turned on inside the toad that you didn't mean to.
I did this for our Ford Fusion we tow, and it works great.