Jayesh,
As you rightly observed activating Cost centre Scenario will hit the performance and will have impact on other standard transactions like FAGLB03.
So have to think again the usability of FIN_CCA in your leading ledger.Doesnt the CCA itself won't serve the purpose.
From my understanding , yes you can switch on or off Cost Centre Scenario at a later stage. But does it worth?
Regards,
Dareal