The trait may or may not be advantageous. Diversity is. In this case the selective pressure is poaching, but selective pressures are constant. Diversity is a bank of genetics that the population can draw from to adapt and survive.
Traits that are rare, are often rare because of shortcomings. But if environmental changes make that tradeoff worthwhile, it can be made. Meanwhile, evolution doesn't stop. Once the trait/gene is common there is positive selective pressure on complementary genes. Over time, these may mitigate or compensate for the negative traits that have acquired.
Of course, on the timescales that humans tend to selectively pressure species, there isn't time for all this elegance to emerge, usually.
Later on they mention that if this genetic trait gets passed on to males, they die. So along with hunting, males are doubly at risk.
It may be advantageous for the survival of an individual to be born without tusks, but it doesn't sound too good for the survival of the species.