I realise this question is a bit old, but I think I can shed some much-needed light on the question.
The non-repudiation value in the keyUsage attribute relates to the whole certificate, not any purpose in particular. The presence of the non-repudiation flag indicates that the private key has sufficient protections in place that the entity named in the certificate cannot later repudiate—deny—actions they take with the certificate. The presence of the flag doesn’t prevent repudiation, rather it indicates that repudiation isn’t likely to survive reasonable scrutiny.
So in this specific case, the CA is giving the user the option of a certificate that does or does not include the non-repudiation element. If you want to assert to those verifying the signature that you can’t easily deny it was you who signed it (the USB token is the key enabler here), use the non-repudiation certificate. Otherwise, use the certificate marked for digital signatures. (Depending on the other attributes in the certificate, you may or may not be able to sign documents with either or both certificates.)
See Wikipedia: http://en.wikipedia.org/wiki/Non-repudiation
See also the relevant RFC: http://www.faqs.org/rfcs/rfc3280.html (section 4.2.1.3)