When I saw the memorial on the edge of town near Tallin in 2007 it wasn't in good shape. I think some resentment runs deep. The german graves are well tended. I don't think there is any deeper sub-text, its just one is a brutalist war memorial and the other is a more personal thing of headstones.
The collection of "we don't need a lenin statue" nearby was cool. Lots of standard-pose, lying on the ground. I think the estonians were careful to dismount these but not (if you will excuse the metaphor) 'desecrate' them because .. well.. there are sensitivities.