Step 1:
To disable the use of Sofort for future transactions.
1) Navigate to Settings > Configure Chargebee > Payment gateways > Smart Routing.
2) And click the pen icon to remove the payment gateway associated to it. 
Step 2:
To disable Sofort payment option from gateway.
1) Navigate to Settings > Configure Chargebee > Payment gateways .
2) Disable to the Sofort option highlighted in the screenshot below from the gateway settings page.
Note : This action would disable the flow that handles Sofort payments.