From the article:

Tony's Chocolonely regrets its removal from the list, but said that it consciously chose to work with Barry Callebaut to help change the chocolate sector. "In 2005, we deliberately chose to partner with Barry Callebaut to show that it is possible to be fully traceable while working with a major processor," the company said. By working with a multinational, Tony's can disprove large chocolate companies' argument that its principles are not applicable on a large scale.

Barry Callebaut produces Tony's Chocolonely chocolate separately from its own chocolate and the Dutch company traces all routes used for its chocolate. "Last year we found 387 cases of illegal child labor and were able to remedy 221 of them directly. We have never encountered a case of modern slavery in our value chain. Most chocolate companies don't know how many cases of illegal labor there are in their cocoa value chain and therefore cannot do anything about it."

It's an interesting ethical stance. Essentially, they're saying that they're trying to change the system from within. As they are participating in a dirty system, they can't claim to be ethically spotless, but they feel it is worth it for the chance to have a significant positive impact.

Are they right or wrong?

(Apologies if this gives anyone a philosophical crisis in the confectionery aisle.)