[just_me]

A million thanks Jon! Your solution to use the if statement works like a charm.
I'll restate it in case anybody wonders which solution I used.

Put the following code in the template where the problem occurs.

{if $smarty.server.HTTPS ne "on"}

Here goes the script you want left out under https

{/if}

Don't forget the {/if} !

With this I was able to remove all the affiliate links, banners etc from showing on my secure pages (cart, checkout etc), causing the pop-up warning about secure and unsecure elements. My https pages now proudly show the golden lock up top of the new IE 7 browser and opens the https page without problems.

Happy New Year!