Hi Tomas,
You are right in your assumption, the Auto Link Tracking setting controls both the download and external tracking. If you only want to set the external linking tracking to false, leave that setting to true and do the following:
1. Create a JavaScript code extension
2. Scope it to your SiteCatalyst tag
3. Paste in this:
s.trackExternalLinks=false;
This also assumes that 's' is the value for yoiur 'S-Object Name' in the SiteCatalyst tag config. If it isn't you'll need to replace it with the correct value.
This will override that setting and you should be good to go. If this doesn't work, please contact your Account Manager so we can take a closer look at this.