Even if you use a centralized node, this kind of centralization in LN is not as bad as the typical "centralization problem" often referred to in cryptocurrency, because it doesn't mean counterparty risk. The worst thing that could happen is that you have to wait some time to get your money back.

BTW a follow-up to the story you link is this one: https://cointelegraph.com/news/guy-who-lost-4-bitcoin-has-re...