You can add additional source directories based on scala version by adding to the unmanagedSourceDirectories setting.
Something like this:
unmanagedSourceDirectories in Compile <+= (scalaVersion, sourceDirectory in Compile) {
case (v, dir) if v startsWith "2.9" => dir / "scala_2.9"
case (v, dir) if v startsWith "2.10" => dir / "scala_2.10"
}
Should allow you to have three directories:
src/main/scala # both 2.9 and 2.10
src/main/scala_2.9 # source only for 2.9
src/main/scala_2.10 # source only for 2.10