If your site defines <link rel='canonical' .../>, you can set this value to true to make Chartbeat use the canonical path instead of the actual URL:
_sf_async_config.useCanonical = true;
This is a good way to ensure consistent and clean URLs across tracking tools. Google has a good introduction to canonical links here.
Alternatively you can use the path variable to explicitly set the path that you want visitors to a given article to ping with. For more on the setting the Canonical and Path variable, check out page 4 of the Getting Started Guide.
Note: Off-site canonical links, i.e. links pointing to other domains than the page is on, is not supported at the moment.