Java is more than a language - it is a platform.
So whilst gcj can compile Java to native code, without support for AWT, etc, it will not run/compile applications designed to run on the Java platform.
I don't know the status of open-source AWT replacements. I know that there are full Gnome and KDE bindings for Java, so you can write Gnome/KDE applications in Java and compile them natively if you so desire - these apps are obviously not for the Java platform either - much like an app written in Visual J++ using the win32 Java bindings is not a Java platform application.
What the Amiga needs, is a Java Platform implementation, even just a runtime. A Java 1.4 implementation would be great... but unexpected.