That cylinder is not just for the 3-point.
That cylinder is on every tractor of that type frame regardless if it came with a 3-point or not.
From the factory, there would have been a standard rockshaft in place of your 3-point rockshaft, that obviously would not have had the upper lift arms.
The reason being is that it is still needed for mower deck lift, as well as a few rear attachments that bolt to it on the ends...like the 30 tiller lift brackets for instance.
What I would do is as I stated before. Cap the lines, and take the cylinder out until I was done painting if I REALLY wanted to take it all the way out. Most likely, Id just cover it with a heavy plastic and set it aside, off its mount.
There really is no reason to run without that cylinder in place, or with the entire 3-point off the tractor...which makes me wonder...did you not have to long "straps" that went from the sides of the rockshaft (two small pins) toward the front of the tractor to two brackets that pivot?