Soft rejected - Theme shouldn't call wp-load.php. Need help

My theme was soft rejected for the following reason;
Theme shouldn’t call wp-load.php read

I guess this is a new change as this was not for our already submitted themes. This makes it difficult to change the values via theme options. The method they mention in the above link is good only if the theme options have only a few options which is not our case. We are using this wp-load for our custom CSS page color.css to control many of styling options for the theme.

Any alternatives/suggestions on tackling this issue?