There are some proteins that directly cause lysis (called "lysins"), e.g. there are lysins taken from bacteriophage (viruses that attack bacteria and are generally species or strain specific) that do kill bacteria effectively.

One major issue with chemical antibiotics (proteins or small molecule) is evolution. Antibiotic resistance is largely the product of the wide and incomplete treatment of bacterial infections, and the resulting emergence of resistant strains. Another issue, shy of evolution of genome modification, is simple gene / transcriptional regulation, and up-/down-regulating surface proteins and sugars that can render such proteins ineffective. It's not as simple as binding a protein target.

Consider that resistance to a novel antibiotic has been observed after a year or two on the market, and it doesn't make sense for a pharma company to invest in bringing one to market.

One interesting avenue is using bacteriophage to treat infections directly. The phage evolve with the bacteria and have a much higher chance of remaining effective. Treating with an antibiotic, or multiple phage, using different mechanisms, decreases the chance of evolving resistance. Phage have been used in eastern European countries for ~ a century, but were dropped in western countries in favor of small molecule antibiotics. There are several clinical trials to bring them back to market.

To bring it back to the article, interestingly phage don't seem to be mentioned, even though they are the most abundance organism on the planet. Surely something has figured out how to eat them...