Chris,
There are 9 matches that you want to exclude and it is possible to achieve this. If the best three teams are 1 to 3, and the bottom three are 11 to 12, then in the following (column balanced) round robin, all 9 of these matches occur in the top left hand 3x3 sub-square - so you need to use rounds 4 to 11 for your schedule. An inevitable consequence of doing this is that 9 matches between relatively closely matched teams (see the top right hand sub-square are also excluded).
Hope that helps,
Ian.
( 1 12) ( 2 11) ( 3 10) ( 6 7) ( 8 9) ( 4 5)
( 3 11) ( 1 10) ( 2 12) ( 5 8) ( 4 6) ( 7 9)
( 2 10) ( 3 12) ( 1 11) ( 4 9) ( 6 8) ( 5 7)
( 4 10) ( 7 12) ( 5 9) ( 8 11) ( 1 3) ( 2 6)
( 4 7) ( 3 5) ( 2 8) ( 6 12) ( 1 9) (10 11)
( 3 8) ( 2 9) ( 6 10) ( 1 7) ( 5 12) ( 4 11)
( 1 6) ( 4 8) ( 7 11) ( 2 3) ( 5 10) ( 9 12)
( 8 12) ( 9 10) ( 1 4) ( 5 11) ( 2 7) ( 3 6)
( 9 11) ( 7 8) ( 5 6) (10 12) ( 3 4) ( 1 2)
( 2 5) ( 6 11) ( 4 12) ( 3 9) ( 7 10) ( 1 8)
( 6 9) ( 1 5) ( 3 7) ( 2 4) (11 12) ( 8 10)