That's actually not a bad idea. Right now yes, it is on when the water in the solar collector is above the set temp of the aquastat. If the temp gets below that, it shuts the pump off. I could prob build a similar controller with an Arduino, but i don't know if it would really be worth it. Even on a very cold winter day, as long as the sky is clear it works and is hot enough to stay on continuously (once every thing heats up) maybe having a controller like you talk about will help it get up to temp faster though.How are you controlling your pump? From what I read it sounds like just with a thermostat so it's on or off.
I built my own controller and use a central heating circulating pump.
To maximise solar gain I control the pump by turning it on and off with varying duration depending on the temperature difference between the tank and the collector.
i.e. if the difference is only 8 degrees then the pump is on 8 seconds, off 2 seconds. When it's 3 degrees it's on 3 seconds, off 8.
Over 10 degrees it's on permanently. This way I get maximum absorption without the complexity of a PWM controlled pump.