Commons Configuration do manipulate configuration files.
Even it gives an option to save the manipulated properties in a new file also.
PropertiesConfiguration config = new PropertiesConfiguration("usergui.properties");
config.setProperty("colors.background", "#000000);
config.save("usergui.backup.properties);
Refer following link
http://commons.apache.org/configuration/userguide/howto_filebased.html#File-based_Configurations
Even, Apache Ant can also help you in manipulating the existing configuration files using your own PropertyHelper Implementation.
http://ant.apache.org/manual/properties.html#propertyHelper
EDITED after response in comments
Apache configuration do provide extensibility using bean Factory , you need to create the Apache config file httpd.conf domain class yourself , to make it working.
Defining the Apache modules in java you can have a look at Netloony source , service/apache/modules to have an idea on this.
http://netloony.sourceforge.net/userguide/intro.html
In netloony the config files values are presented in JTable, you need to use any configuration framework to persist it in file.
Hope this helps, I understand there is nothing out of Box in java presently to read apache conf files. I was trying to give a pointer where you can start with..