Hi Leslie,
I can make that change for the next release, but you can solve this problem immediately without any code changes by adding a couple of attributes on <portal:ScriptLoader to make it not load the jquery scripts then hard code them into your layout.master using the protocol relative urls
on <portal:ScriptLoader add:
AssumejQueryIsLoaded="true" and AssumejQueryUiIsLoaded="true"
then add your own links to the jquery files in the <head above scriptloader
Best,
Joe