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I would leave the connector, it was a moisture seal on it. Snip the two brown wires going to it, connect one side to a good ground, and connect the other to the appropriate wire in the harness. I think you're right saying green/yellow but I don't recall as I'm typing this.
I've done 3 option B mods in the last 5 years and have always felt that the o-ring on the stem of the connector was still effective at help sealing out moisture. No problems so far. Since the wiring to the actual connector has been neutered on both sides of it, I don't understand how leaving it there could affect anything. Can you elaborate? I agree completely that it's not needed as a part of the system, but removing it has a collateral effect of allowing moisture ingress to the inside of the WABCO block.