I will probably work that into refractasnapshot, but I'm not exactly sure how I'll do it. For now, what you can do is make the changes manually, and then set the initrd_image variable in the config file to point to your rebuilt initrd.img, and that one will be copied into the iso image.
And just in case it's not fully clear to anyone reading this, don't replace the initrd.img in your encrypted installation with the rebuilt one that has the cryptroot file removed.