You can replenish channels, even multiple all at once, either through someone just paying you, or an on-chain payment through a "loop". And trading some decentralization for "performance" when dealing with small frequent payments is still better than other choices.

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...