Remember mines are actually sorta expensive, and take a lot more time to rebuild than scouts, so it's not really... THAT bad. Random idea, what happens when you pair flak ships with scouts? The flak might take out the mines more effectively since it has 360 degree firing, so it can react faster.
...A'course, I'd try that myself but Sins has the "decompression error" when I try to re-install it from beta entrenchment. Why doesn't stardock just release a simple utility to clear out all Sins-related files, directories, and registry entries rather than ask the end-user to hunt through their system for these little things? A utility that does that would take almost no effort... I'd make it myself but I'm busy with work that I actually get paid for.