If you have a "bang-bang" controller as some here have called it, why not try this instead.
Use the controller to pull in a decent double-pole relay connected BEFORE the bridge rectifier, that is, on the "raw AC" side.
When the battery volts get high enough to trip the dumpload, the load is applied to the output of the MILL ONLY, and NOT the batteries.
If the mill is making only a small amount of power, thats all that can be shunted.
A failure of the controller cannot flatten your batteries, the worst it can do is stall your mill so the batteries cannot charge (but you'd see no amps flowing and know why quickly enough)
Can be done with a minimum of rework of your existing setup, although it would require one or two more loads (resistors).
Happy to knock up a sketch of the circuit if you need it.