I wish I had seen this before you had to resort to such extreme measures.
I too have had the same problem you described in your opening post.
I rather simply fashioned a home-made tool comprised of: a 30 in. length of 5/8 in. black pipe from Home Depot, and a couple of spare 6-32 nuts.
At one end of the pipe, I attached the 6-32 nuts on opposite sides of the pipe (I think I epoxy'd them in place, but I don't remember).
See the attached close-up pic of the end with the nuts attached. (never mind the empty holes in the pic. They were already in the scrap of black pipe that I just so happened to pick out). I may have also had to round the nuts off a bit, in order to enable a nice snug fit in the final application.
Anyhow, sliding the length of pipe down over the damping rod piston shaft, until the those nuts slip into a corresponding pair of slots in the damping rod cylinder, allows you to hold the damping rod cylinder from turning whilst you remove the bolt from the bottom (I just used a channel-lock pliers to hold the black pipe from turning, which in turn prevented the damping rod cylinder from turning).
Make sense? Hopefully it made sense.
EDIT: As I think back about this, I can't remember if I used this on my RC51, or my CBR1000RR, or my ST1300, or all of em. I've done fork seals on each of those, and others, at some point. In any case, although dimensions may vary, the same concept applies.
Looking back in my RC51 service manual, I see that Honda actually makes a special tool called a "Fork damper holder" - part numbers 07YMB-MCF0101 or 07YMB-MCFA100