Mrbacklash,
I don't know why this didn't occur to me, possibly because given the option, one would remove the clevis end first, slightly bevel the ID and then push out the piston and rod. But, although for several reasons, some previously mentioned and some not, I wouldn't personally recommend doing it with the 9", there is a practical way to cut off the rod and clevis ends without having to pass the 1" rod through the headstock spindle. Cut off the piston end first. I don't know specifically what the clevis end on your cylinders looks like. You may need to make a fixture for the clevis that you can grab in a 4-jaw. but that you would have to do (or not) with any lathe up to maybe a 20". You will in any scenario have to have a steady rest. Be sure that it is the type that the top opens so that you can just lay the cylinder down on the bottom two jaws. And I would recommend roller jaws.
The Atlas tailstock ram is 1-1/8" in diameter. Remove the ram, feed screw and bearing. And the ram lock. Sleeve the tailstock with a length of 1-1/8" OD .06" WT thin wall tubing. You might drill oil holes to line up with the hole that the ram lock sleeves normally occupy. You will also need something to keep the sleeve from rotating in the tailstock. Remove the anti-rotate screw from the bottom of the tailstock nose. Get a dog (extended) point socket set screw that fits the anti-rotate screw threads (probably 1/4"-20). Drill a hole in the sleeve the same diameter as the dog point to line up with the tapped hole. Install the sleeve and run the dog point screw in until finger tight. I would probably secure it with Blue Locktite. With a Dremel or similar grinder and as large stone, grind the dog point down flush with the ID of the sleeve. I have a Dremel tool holder that fits the vice on my milling attachment that I would use for the job. But if you have steady hands, you can probably do it free-hand. You want a slip fit between the rod and sleeve so you may need to ream or bore the sleeve in place after you have it locked.
Anyway, this would work if you don't buy one of the larger spindle bore lathes. Regardless of what you use to do it, you will need to make a slip fit plug to keep from egging the cylinder during cutting off of the second end (whichever end that is).