I believe this is already possible, unless I understand you wrong.

Take for example: https://obsidian-html.github.io . Note that there is no folder Resources in the root, even though I have that folder in the root of my vault (and use notes from it).

Note that path Resources/ is not in exclude_subfolders: https://github.com/obsidian-html/obsidian-html.github.io/blob/7c032dcac417db4e6ef80470bc7c3f1061e6d0d2/__src/config.yml#L60
(This setting just blocks any file from a path from being included. And by default has paths such as .git, .obsidian, etc.)

Compare that with toggles/features/create_index_from_dir_structure/exclude_subfolders:
https://github.com/obsidian-html/obsidian-html.github.io/blob/7c032dcac417db4e6ef80470bc7c3f1061e6d0d2/__src/config.yml#L247
This setting does contain Resources, and it also has another setting below it to exclude certain file paths as well.

So if you don't have a setting in your config yet for toggles/features/create_index_from_dir_structure, copy the block below, and adjust the paths for your usecase. That should solve your issue.

toggles:
  features:
    create_index_from_dir_structure:
      enabled: True
      exclude_subfolders:
        - ".git"
        - "__src"
        - "md"
        - "obs.html"
        - "assets"
      exclude_files:
        - "favicon.ico"
        - "not_created.html"

Default settings file: https://github.com/obsidian-html/obsidian-html/blob/master/obsidianhtml/src/defaults_config.yml

Note that wildcards, glob patterns, etc, are not supported. So at the moment you have to add 1 line for each assets folder that you want to exclude. If I understand you correctly you have multiple of these folders.

It should be relatively easy to add something like a glob pattern support to exclude all asset folders in one go. If you could use this, please make an issue for it, then I will add it in the next release.