As a CS superior, how would you handle a CSR who is working perfectly in an innovative way BUT without following silly routine instructions?

Thanks for the question.

If there's a SOP that must be followed every customer interaction (KPI), what the CSR does is insignificant because at the end of the day, the scorecard is the final basis of performance. 

Hmm..If its silly instructions, then why at all have it.  Remove them, and you won't have to bother. 

We define Processes to have repeated success in your business. But these are not to be taken as a Bible rule; and can be altered based on need. If the Innovative method are working better and if can be repeated again and again for success...add them in the process. Else, forget it.

CSR jobs is a routine work and if we don't have variety in handling calls, but adhering to corporate governance without putting company at risk, it is okay.