Hmmmm...
I suppose you could open up the "setuplevel.fpi" script and remove the save option from the "pause menu", then use the "quicksave" or "save" commands in a triggerzone script positioned over the start marker of each level and over any checkpoints. Remember that "save" will pause the game and ask for a slot.... though, I don't remember if QuickSave does the same.
I'd be safe about it and just use quicksave for all of them. If it doesn't do what I think it does, then it looks like I found another thing to add to my Mod.
The one and only,
Those who live in the past, are destined to insanity. Those who live only for the future, will be slaves to their ambitions.
Those who live in the moment... only they, are truly happy.