I use a heat gun to make things hot... but yes, you can damage the seal. BUT... sometimes you don't have a choice.
One other thing to try... while you keep pressure on it.... have someone tap on the PTO with a metal hammer. Sometimes, the vibration will help break the rust/corrosion that is holding it on.
I did an engine last year that I thought I was going to break the piston because I had to put so much pressure on the PTO. I had it out, and bolted to a bench... and when the PTO popped loose... I fell, and hurt myself. And... the way it popped... I thought I broke one of my table bolts. But, when I checked... it was the PTO.
They can be very stubborn.
If the splines aren't ripped out of the PTO, you may be better off using an impeller tool, since the chain wrench gets tighter, the harder you pull. (could be compressing on the threads)