If you are looking for MVC then you have many choices, here i am suggesting you two of them
1. Follow MVC in your current running Project.
a) create a controller servlet that will decide the flow
b) For all the business logic create beans and access these beans in your JSPs
c) All the presentation includes in JSPs using EL or JSP tags or scriptlets
i don't think that using scriptlet in JSP is a bad thing. But you must not put your business logic in JSPs or big codes should not be placed on JSPs. If you need some small codes just put in JSP. I agree that scriptlets should not be used in JSPs but it can be used for small codes.
2. Follow Struts:
Its a good practice to follow struts framework. This framework is based on MVC architecture. It make the system robust, powerful and well designed.
Please correct me if i am wrong at any point