There are many reasons why a joey can be rejected, it is not necessarily because of genetic issues (the female can be too young, not have enough milk, there can be conflicts in the colony, stress of any kind or the parents may simply considere that the environment is not good enough to raise joeys).
Our gliders are also mostly outside of natural selection, precisely because they are raised in captivity, I tend to think that 80% of the gliders would not have survived in the wild.
Besides, there are no such things as good and bad genes actually, there are positive or negative combinations between different genes and environment. I think that people put too much credit and beliefs into genetics lately, as if it was the essence of everything, and neglect other parameters (and epigenetics).
The short answer would be, allowing a rejected joey to survive is not a problem if he doesnt reproduce, and is not necessarily a problem if he does either at the condition to avoid inbreeding. (add to this that eliminating the joey from the breeding pool would not erase the "bad" genes from the pool, since those genes are from his parents who have to be carriers, and other joeys from the same couple are also likely to be carriers)