The only built in way I can think of doing this would be to add the Custom Options to the configurable product and not the simple products associated with it.
I’ve done so with floor mats that are available with or without embroidered logos, for example:
The downside is that if only some of the simple products associated with that configurable product allow the custom option it will still be available for all the products in the configurable product.
A fix for the situation I listed above, where only some products within the configurable product have custom options, is to simply make a new product attribute, and make more simple products to fit that configuration. So instead of custom options you will have an extra configurable product dropdown.
For example: consider the following configurable setup using custom options:
-Red T-Shirts with Custom Options of White or Black Logos
-Green T-Shirts with Custom Options of Yellow or Blue Logos
Obviously couldn’t add a Custom Options list with all 4 logo options, otherwise you’d get a Red T-Shirt with Blue Logos which doesn’t exist. The solution to this is to make another product attribute and more simple products to fill those options.
You’d add a new dropdown product attribute with the options for all color logos (and a “No Logo” option if it is available as so)
So instead of using Custom Options with your configurable products, you would make one configurable product with both shirt color and logo color attributes, with the associated simple products being:
-Red T-Shirts with No Logos
-Red T-Shirts with White Logos
-Red T-Shirts with Black Logos
-Green T-Shirts with No Logos
-Green T-Shirts with Yellow Logos
-Green T-Shirts with Blue Logos
Now when the customer chooses Red T-Shirts, the Logo drop-downs will only show No/Black/White Logo configurable options, and the opposite with Green T-Shirts. It’s a bit more work but it looks better and behaves appropriately.
For better illustration here’s a more complex configurable product on our website, using only configurable product attributes, no custom options:
It uses 5 different configurable product attributes to narrow down the selection, no custom options are used. Keep in mind there is an associated simple product for every conceivable combination of options, and the dropdowns will change depending on what is selected before it. It is very important that you order the configurable attributes correctly, starting with the most general option first.
I hope my experience in dealing with configurable products helps you out.