Most of those should be bacteria, not a virus. I would speculate that they would be much easier to treat with common antibiotics. After all, they haven't had time to adapt and become drug resistant.... Yet.
In the linked experiment, it takes bacteria 11 days to evolve resistance to 1000x the concentration of antibiotics normally needed to kill it. This is basically the concern with overuse of antibiotics in healthcare, hygiene products, and livestock - that 0.001% of bacteria your soap doesn't kill is basically the Superman of bacteria, and you just killed all its competition, leaving it free to replicate into its own little army.
A high enough dosage of literally anything is toxic / eventually fatal for humans, so we can't just keep upping the concentration of antibiotic medication. There's even a term for it - "post-antibiotic era", which we're already knee-deep into.
Anyway, yeah most ancient microbes would be absolutely destroyed by all the modern natural and artificial means that have developed to kill it... the catch being that if the microbe is old enough, things haven't developed to kill it, so the current state of our immune systems and medical tech could amount to an all-you-can-eat-buffet for something that didn't develop adjacent to us. Combine that with a few weeks of petri-dish-experiment of ancient microbe incubating in some immunocompromised old man who decides he's tired of staying home sick and wants to go out christmas shopping for his family... and now we have a problem.
Nah. Not worried about microorganisms. The way our immune system works is that it stores the "fingerprint" of pathogenic bacteria and viruses and this data is passed down to our progeny. So, we already have built in immunity to 1000 year old pathogens. In addition, vaccination has also "side loaded" many pathogen's fingerprints.
That... doesn't make any sense. If what you said was true, every baby alive would magically have immunity to everything any human has faced ever and would never get sick. Kids are CONSTANTLY sick.
It's actually better than what OP said. We have a T cell for every antigen. Period. Even the ones that nobody has ever encountered. That's because T cell receptors are proteins, that is, combinations of amino acids. Random combinations of T cell receptors are produced by the immune system (if it does not harm the host).
The caveat is that it takes a while for the T cell of an unknown antigen to be activated, enough time for the sickness to appear and even become critical.