Not sure if it’s still in time but this might help all of you who are having the same problem, as I had:
Create a file ~/.gtkrc-2.0 and add this content to the file:
style "eclipse_fix"
{
base[ACTIVE] = shade(0.7, "#4283d3")
}
class "GtkTreeView" style "eclipse_fix"
Then just set Unity a new theme (in Configuration > appearance) and set again to the previous theme (Ambiance for instance). That will read the new file created above and the new color will take effect in eclipse.