Essentially, when an animal species reaches this point of re-population, it is in the best interest of the animal to be protected by state efforts rather than federal - aka ESA. The ESA actually can hinder the local efforts to relocate and protect small, pocketed, encroaching/encroached upon groups - which will, sadly, be killed off by disease, human action (outside those wanting to help). While the ESA is a good thing for a species that is very much in danger of extinction, it does not really help a group that is no longer at risk of extinct, but that is at risk from the perils of re-population into an environment that no longer is setup to hold the same size groups as before.
Also, as I failed to see this mentioned in the provided material, as far as I know (and this could be skewed due sources, please let me know for sure), the removal is not universal. But allows for exceptions for certain states.
While I do not personally agree with removal for certain states, and I do want to see the species protected in some way, I feel that the ESA is no longer the best possible protection for the wolves. And that action within the states as opposed to Federal would be in the best interest. So a petition to the congressional body of the states in question would go farther for the animals than a petition to the US Congress.
Just my take on this, having been thinking about it since reading the news last week when this came to light.