Bear in mind most of these subspecies live in isolated populations so would naturally breed with siblings/parents. Also bear in mind that Reptilian DNA is a simpler chain than mammalian and keeping a chain pure can actually prevent deforimities etc (see the study on cunninghams skinks as a good example.)
Also couple the above with the very limited bloodlines outside of Oz.
The only time I can foresee future problems is when interbreeding snakes (and other reptiles) with weak/defective/abnormal genes. 'Morphs' for example.
Out of interest what problems do you see?