I believe that you already went for one or the other option by now. Anyway, comment might still be useful for others.
As WhiteFang wrote, using MVC is the only highly recommended suggestion.
If your application is a web based one, JSP would most likely be a better option as it is better known and one can write quite clean presentation code using JSTL (just make sure you don't mix in scriptlets ... all data should be prepared in servlets and passed on to JSPs as attributes). Choosing JSP you bring value to the project by enabling managers to plug-in easily other developers when needed to deliver faster etc.
Anyway, since you already have it on FreeMarker, if the template looks ok already, I wouldn't change it. Rather wait for when you have a business reason to switch. Whatever well designed an application might be, it will eventually need to be partially or even fully rearchitected. As long as you do modular programming, and keep your transformation in an isolated module, you will be able at any time to easily switch to whatever technology you'll see fit (potentially a new one, better than FreeMarker or JSP :) ).
I am usually using FreeMarker for non web applications. Or even in web applications, when I need to generate notification emails for example, which don't need to be web enabled. Otherwise JSP works great so far.
Stef.