Synthetic supermicrobe will be resistant to all known viruses

That advantage only goes so far:

• Plenty of nonviral bacteria-eating entities exist, and would become more numerous
• Plant and antibacterial defenses aren't viral-based
• For the bacteria to compete in the same niche as unmodified versions it has to fulfill a similar ecological role: photosynthetic cyanobacteria with altered DNA would still produce oxygen and provide food
• It couldn't benefit from exchanging genetic material with other kinds of bacteria

Well, it sounds like their dietary requirements would prevent that. Of course, if it's possible for someone to design a symbiotic system that outputs those four amino acids, then there could be trouble. Hopefully that's not feasible.

I think that most biosphere will be eaten one day by a replicator, which will be created by a biohackers just for fun. And this bacteria shows new way how to do it. I thought before about universal virus which is able to infect all types of cells as a way to "eat biosphere".

Insanely dangerous, yes, but then again so is all potentially world-changing technology (think AI and nanobots).

In other words I agree with you, but I think that the response to "new technology with potentially horrific consequences or otherwise high risk/reward ratio" should be, "estimate level of caution necessary to reduce risk to manageable levels, double the level of caution, and proceed very, very slowly."

Because it seems to me, bad at biology as I am, that the ability to synthesize arbitrary proteins, which this technology does/is a stepping stone to, could be incredibly powerful and life-saving.

So far as I know, no animal, plant, or fungus's defenses against bacteria rely on infecting them with viruses. The only losers in this are viruses.