The analogy is that neither side is desirable yet an outside force for good has to choose between the lesser of two evils...yet any compromise between good and evil is a victory for evil.
By that logic, any compromise with any civil authority would be "a victory for evil" since any civil authority is a greater or lesser evil. Until the Lord returns, we'll have to make do with some degree of compromise.
...and dont forget that the Catholic Church persecuted Galileo for agreeing with Copernicus...the church couldnt handle the truth!
In Galileo's day, none of the scientific authorities believed him either, because he made his claims with no data. Beyond that, he was pompous about it; he had been instructed to not forward the theory without proof. The imprisonment happened after he launched a personal attack on the Pope, who had at a point before that had actually assisted Galileo.
Late in his life, Johannes Kepler used the data that Tycho Brahe had collected -- but even though Galileo had been "right" about heliocentrism, he was still a pompous ingrate. Not only had he insulted his former supporter, the pope, he rejected Kepler's theory because Galileo preferred circular orbits while Kepler hypothesized elliptical ones (based on real data!).
The "Catholic Church persecuted Galileo" meme is very tired, and giving it credit requires one to suspend disbelief.