Can a second mass extinction by microbes happen?
First of all, let’s consider your Methanosarcina scenario in specific.
Methanosarcina with those properties are still around. So, there is no reason to expect that introducing some ancient Methanosarcina into a suitable environment today would do very much – as they should already be there. Any existing (large-scale) environment providing a niche for Methanosarcina should already be occupied by it as it only needs a single organism to get there by chance at some point.
Moreover, there must be some reason why our atmosphere stopped being filled with methane by Methanosarcina.
For example some prerequisite resource could have been depleted, some other organism evolved that consumes this methane or controls the Methanosarcina population by feeding on it.
Whatever this reason is, we should expect that it still applies: A required resource would still be gone and a second organism controlling this activity should still be around (or resurface together with the Methanosarcina in question).
In fact, the hypothesis you mention maintains that the nickel required by Methanosarcina to produce methane was available in huge amounts due to specific volcanic activity at that time.
Finally, the current ice masses of the Earth are much younger and have not been around since the Permian period.
In general, if geologically cryostoring microbes were relevant, climate change should be the least of our worries as drilling a hole into the ice or local geologic activity could suffice to bring back a few individuals – which is all that would be needed.
Now, what about unfreezing microbes in general?
Due to lack of fossils, we have little knowledge about microbe extinction, except that it does happen.
However, my ecological intuition is that microbes either lose their niche to a fitter alternative (which either be more apt at causing problems or avoid them resurfacing) or survive in small amounts (ready to occupy their niche if it should resurface).
Microbes are considerably different from higher, sexually reproducing life forms here as it only needs a single individual to revive the species and individuals can survive for a long time in adverse conditions, not only by sporulation but also because they need little energy to maintain their state.
Finally, if a niche for disastrous microbes exists, there is the constant risk that it will be filled by some ordinary microbes evolving, which brings us to the next point.
Something that is conceivable to happen is that some microbes spontaneously evolve to fill a big niche and have some disastrous by product leading to a mass extinction.
It is hard to estimate this risk, but as far as I know, there is no historic precedent after the evolution of higher life forms.
(As elaborated above, the Methanosarcina hypothesis for the Permian extinction features additional factors.)
However, I consider it unlikely that climate change increases this risk.
While climate change undoubtedly has disastrous ecological consequences, tilting individual ecosystems, I don’t see how it creates some fundamentally new environment (that wasn’t already there in similar form somewhere else on the planet) that would stimulate a spontaneous disastrous microbial evolution.