You don't have to change the source code of Flexjson to do this. The way to handle this is to create your own implementation of ObjectFactory and register that for the type you are binding into. From there you can instantiate it however, you desire. It's easiest to subclass BeanObjectFactory and override the method instantiate(). In there you can do whatever you want to create an instance of an object you wish. By subclassing BeanObjectFactory it will take care of binding the individual properties from the JSON into your object using the setter/getter of that object. If your object doesn't support property methods you might find it easier to implement ObjectFactory and manually setting the values on that object from the JSON. There is lots of documentation on the Flexjson website about building ObjectFactories.
Then you can register your ObjectFactory to that data type using:
new JSONDeserializer<SomeObject>()
.use( DateTime.class, new DateTimeObjectFactory() )
.deserialize(json);