You can pull them out without harming anything. You don't really grease the rod, it rides in engine oil. You do want the put a light coating of grease on the part of the rod that sticks outside the motor though. It's usually just plain steel and will rust. Eventually, chain fling-off will coat it but before that happens, it could get rusty. Then you'd be pushing rust through your seal every time you pulled the clutch in.
That discoloration might be the seam between the rod and a hardened steel cap on it's end. I don't know for sure about the early 650 long rods but some other Yamaha models use an alloy rod with hardened steel end caps. I think that was done so the rod expanded at near the same rate as the engine cases when things heated up. That's a problem with the all steel rods in the 650. They expand less than the alloy cases so you get increased freeplay in your clutch lever as things get hot.
