Regardless of how you cut it, you will have a raw steel edge. But it will cover over with carbon fairly quickly so I would not worry too much about rust.
If you break thru the chrome, and you have a new blade, you can cut them with a hacksaw. Probably don't even have to break thru the chrome. Hacksaw blade should eat right thru it. Put a band clamp on them at the cut line and use it as a guide.
Your cutoff disc with do a good job if you have a steady hand. You can alway use it to clean up the end when you are done.
I understand your desire for a nice clean and square cut. I'd be the same way. But if it is off a bit, the muffler will not care and nobody will see it. It will only keep you awake at night.