Why shouldn't the AFL prop them up? They prop up the Swans, Lions, Giants, Suns, and other Melbourne teams.
The league props these teams up for the greater good of the league (generally to maximise TV money and exposure over the long term). At times that may include support for teams in SA too. Remember that the money the AFL has comes from the clubs in the first place, no clubs, no fans, no AFL!
That said, the SA situation is not working as well as it should. The SANFL and the clubs really do need to structure themselves in a sustainable way. Find a way to make the two club structure work better.