I had somewhat similar problems and wrote a library to solve it: 
 https://github.com/timboudreau/scopes (you can pick it up from the Maven 
repo here: http://timboudreau.com/builds/ )

Basically you should just be able to do something like

ReentrantScope myOtherScope = new ReentrantScope();
// in your binder
myOtherScope.bindTypes(binder(), ApplicationConfiguration.class);

then when you have your instance:

try (QuietAutoCloseable ac = myOtherScope.enter( theConfiguration )) {
     // do what you need to 
}

The pattern I wind up using this for (not a servlet environment) is to take 
a scope's contents, and sort of freeze that, throw some work on thread 
pool.  To make that easy, there is  ReentrantScope.wrap(ExecutorService), 
which gets you an ExecutorService which will freeze the scope's contents at 
the time a Runnable/Callable is submitted, and then reenter the scope with 
the same contents before the submitted code is invoked.

All that being said, if you have the objects that would be injected to run 
whatever needs the ApplicationConfiguration, it may be simplest to just 
call what you need to call - in other words, be sure that injection is 
buying you more than the complexity you seem to be adding to do it with 
injection.

-Tim

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