I've been able to achieve what I wanted by instantiating a ClipsFilesExportProjectPlugin
object within my own plugin. With this you can specify the name of the pins and pont files and execute the export so you have a copy of the file on disk and do what you need with it. Pretty ugly but achieves what I needed it for.
ClipsFilesExportProjectPlugin p = new ClipsFilesExportProjectPlugin();
p.setFiles("temp.pont", "temp.pins");
p.exportProject(getKnowledgeBase().getProject());
File pontFile = new File("temp.pont");
File pinsFile = new File("temp.pins");
// do what you require with the pins (and / or pont) file
pontFile.delete();
pinsFile.delete();