Well, it was a somewhat educated guess. I haven't actually tried it myself. It's just that I remember reading in the installation instructions for 1.1.8 to make sure the 1.1.8 class directories appeared in the class path before any other directories.
So... one could assume that if you put the 1.1.8 directory before the 1.3 directory in the class path, then the Java apps you run will always look in the 1.1.8 directories first.
This should not disable 1.3 support because when a java app tries to load a class that does not exist in the 1.1.8 directory, it should then look in the 1.3 directory. Oh, wait.... not sure what would happen if there are 2 versions of the same class. A 1.3 app finding the 1.1.8 version of a class might produce unexpected results if it loads at all.
I haven't looked in the ini files to see if there's any kind of entry that determines default Java version.