One thing I've learned in the time I've spent with the amnesia editor, is that you'll often run into situations where you're trying to do something the amnesia engine just can't do. In these instances you have 2 choices: give up what you're trying to do and move on, or attempt to improvise. What you're trying to do may not be possible (don't quote me on that) but the solution I offered would work. The player would still be able to save and exit, but once they load their save it'll still start them at the last checkpoint they used.
On a personal note, preventing the player from saving whenever they want is a bad idea, especially if your story is a long one. Things come up in people's lives and expecting someone to either postpone their plans to find a save point or replay a bunch of the game later is asking a lot. If you do go this route, make sure the save points are frequent enough to not be annoying