You have essentially two options, which you have already identified. Basically, you can get a patent on the allowed claims now and file a continuation drawn to the rejected claims (if commercially feasible). Or, you can argue the non-allowed claims and risk the examiner changing his mind re: the allowed claims.
What option is best will depend on a number of factors, including finances. E.g., filing a continuation will require, at a minimum, an extra set of filings fees and another set of maintenance fees should the new application issue. The value of the rejected claims and the relative strength of the examiner's rejection will also play a role in the decision.
So unfortunately, the answer to your question is, "it depends." And without knowing all the relevant factors, it is pretty hard to provide a clear recommendation.