... then the figure will have the same settings when it is loaded back in.

But those won't actually be the default settings, they'll just be the current settings. The defaults are what you see when you restore or conform a figure.

To set the default morph settings for a figure, use the memorize function (Edit menu --> Memorize), and then save the figure to the library.

Oh, and Morph Manager (in Free Stuff) works extremely well at deleting morphs from a CR2.