So content negotiation in practice doesn't use accept: headers except in limited circumstances; for the most part, the sites send some kind of 'active content' or content that autoselects for itself what else to download; e.g., a HTML page which contains Javascript code to detect the client's capabilities and figure out which other URLs to load.
The embedding of scripts in CellML is not recommended, not defined by any specifications, not (as far as I know) supported by any software packages, and if vendors do want to support scripts, they should only use it express functions which cannot be represented in MathML, not for content negotiation. Therefore, scripts are not a viable option for CellML negotiation.
If you have a HTML page that includes javascript that asks IF (browser supports CellML 1.1) THEN (load URL for cellML 1.1 content) ELSE IF (browser supports CellML 1.0) THEN (load URL for cellML 1.0 content) ELSE (insert content for 'can't display model') you don't put the Javascript inside CellML, you put it in the HTML code that decides whether or not to load CellML at all.
BTW I assume you are talking purely about Accept: and not Accept-Language:, as Accept-Language: is widely used by multilingual sites to determine which language to serve.
Accept-language: doesn't have the same scalability problems that accept: has.