yes you can do it, copy your save game folder (the one with the name of your save) to your desktop or so, then you have a back up. do what you want, then when that saves it will not save to your backup. it will only save to the one inside the KSP file. of course nothing else you do will be saved if you revert back to your old save, but btw even if you kill jeb or any of the other orange suited pilots they cannot die. they will always be available in the crew section. orange pilots are the only ones that cannot die. (they die but they will be available again.) (not perma death) as far as mods. I think incorporating a similar practice could allow you to use mods for one save but not the other. you could just remove the mod folder (depending on the mod) as well before loading back in your "vanilla" save. Fyi, I have used this method to make a career mode save with 50,000 science lmao