To counter it, use barrowed time....or Naix rage....Or hookshot/blink/rofl past it into the rearmer...Or berserkers blood...Or flesh heap...Or trigerred heal stacking...Or pipe....or mass illusions/summons...Or invisibility....Or global silence....
This is getting tiring.
Just because you pick 6 rightclicking passives doesn't mean that builds that counter 6 rightclicking passives are broken or overpowered.
If you really can't handle it, make blademail and necro 3, cheap and will always kill the rearm eclipser in the midgame.
Alternatively, use smoke to catch the rearmer off guard. It takes time to set up multiple eclipses over an area.