In most cases, standing makes sense, and would be safer - table saw, lathe, grinders, etc. It would let you stand off to the side so you aren't in line with the blade or wheel.
I can't personally see a problem sitting in front of a scroll saw. The worst event I can think of would be a piece of broken blade flying into your eyes - always wear safety glasses. I have a magnifier light between me and the blade. But, if you are standing, it would be easier to stop cutting and walk around for a break.
In the end, I think it's up to you.
Jim