If reality is incompatible for Star Trek and Trek wants to pretend to be our future, they should probably become compatible with reality instead of the other way around.
This wouldn't work too well: it's akin to DSC having to give up "impulse drive" and adopt whatever NASA decides to fly next year.
Today's science is outdated in Trek anyway, especially when it comes to space stuff. We don't really know anything about outer space that would be relevant to Trek: either it's insufficient (we don't know where the eetees live or how the center or the rim of the galaxy is put together) or incorrect (we mistakenly believe there aren't planets where Trek shows those to exist, and vice versa) or just plain indifferent (so we have now discovered that basically every star has the potential for Class M planets - big deal, we could see that already back in 1966).
Even within the confines of reality, today's method of naming planets is likely to be a mayfly. What we have today is fuzzy guesses from insufficient data; we can't even agree on the definition of "planet". When we are confronted by the complex reality of our universe for real, with better telescopes or stellar flyby probes, we'll need a new naming system again. It probably won't be anything like Trek's, which is based on assumptions of simplicity - but it may end up looking like that anyway.
Timo Saloniemi