The short answer is No, you have the mods installed for all saves or you don't have them at all.
The long answer is you can totally do that, but you have to install the game multiple times. I remember Scott Manly did an episode that covered how he could run different versions of KSP so he could run certain mods that are no longer supported.
Kerbal Space Program - How To Backup Your Old Versions On Steam
He copies the entire KSP game folder and moves it to a repository. Then he just copies the version and mods he wants back to the regular location.
Edit: Copy the folder C:\Program Files (x86)\Steam\SteamApps\common\Kerbal Space Program to another location (eg. Documents). Then when KSP updates you can revert to the old version by copying the file back.