That's because the Church didn't draw distinction between science and theology. As you said, it considered the two to be harmonious. This is why both Bruno and Galileo were persecuted. It did so happen that Bruno had theological disagreement, but the same wasn't true for Galileo. In fact, he was sure that he could talk the Vatican into accepting heliocentrism for the same reason you cited -- he bought into this whole crap that science and religion should be harmonious. He got more than he bargained for.
And it is clear that scientists of the time feared persecution by the Church, because Copernicus waited until he was dead to publish his theories.
You're quite wrong. The church
did draw a distinction between science and theology. In fact, medieval scholasticism regarded different disciplines as
completely distinct, with their own methods and standards of truth (this goes back to Aristotle). The point was that these very different disciplines nevertheless all agreed with each other, because truths cannot conflict. This remained the case in the Renaissance. Bruno was not persecuted for his heliocentrism at all. And the reason why Galileo thought he could argue the church into accepting his views wasn't simply that he thought science and religion are harmonious, but that he thought cosmological theories could be proved. In his case, he thought that his theory of the tides completely proved heliocentrism. In fact he was wrong in that (his theory of the tides was completely mistaken in itself). Galileo was basically an arrogant self-promoter who happened to be right on the issue of heliocentrism, but had far less evidence for it than he thought he did, and managed to alienate all the people he should have been able to persuade. Mocking a hitherto sympathetic pope as "Simplicio" in his "Dialogue" was the last straw.
You must remember that opposition to heliocentrism was hardly confined to church authorities. Even in Galileo's day, the evidence for the theory was hardly overwhelming and most philosophers were not convinced by it. This was even more the case with Copernicus, who had virtually no evidence for it at all. Why should the church have accepted such a minority crackpot theory? The fact that Copernicus had his works published posthumously doesn't entail that he feared ecclesiastical persecution. Perhaps he just feared general ridicule.
I looked into those guys and there's no indication that they did their research at the command of the Church. Rather, they were interested in science before they even became priests and simply continued doing it thereafter. Btw, Riccioli discovered a lunar crater that he named Copernicus crater. Funny how a priest of the time would do that.
The Jesuit order did make a particular effort to contribute to science and philosophy during this period (they opened many free, excellent schools open to children from all religious backgrounds, which taught all the latest material); obviously its greatest luminaries would have been interested in the subject even before joining. The fact that Riccioli named a crater after Copernicus ought to indicate to you that the situation was not quite as simplistic as you suggested before.
The Church has been the center of scientific opposition throughout history. In the Renaissance, it was heliocentrism. In the 19th century, it was evolution. Now, it's genetic engineering.
That statement has more to do with rhetoric than fact. The facts are these. The church opposed heliocentrism while that theory was unproven, but it did not oppose research into the field which sought to discover what was true. When heliocentrism was proven to be true (inasmuch as such a theory can be proven at all), it withdrew its opposition. What's wrong with that? In the nineteenth century, the Catholic Church (at least) didn't actually have much of a problem with evolution per se, although it didn't like what it regarded as the atheistic and materialistic consequences of Darwinism in particular.
This is an interesting article in the Catholic Encyclopaedia, published right at the start of the twentieth century, in which the authors are quite happy with evolution. Most of the opposition to evolution then (and now!) came from
Protestants. And it's very misleading to list genetic engineering in with heliocentrism and evolution, because genetic engineering is not a theory which may be disputed but a practice. When it opposes genetic engineering, the church isn't denying something that scientists know to be true, it's saying that certain practices which scientists may wish to engage in are unethical. And that's a completely different issue.
The notion that "the church" (which people who say this sort of thing always leave ill-defined anyway) has been an eternal opponent of scientific progress is a myth, and a myth with an identifiable origin, too - the work of figures such as John William Draper and Andrew Dickson White in the late nineteenth century. What basically happened is that they looked at the arguments then raging about Darwinism and made the assumption that these were typical of the relationship between religion and science throughout the ages. They seized upon Galileo as a parallel case, ignoring the true facts and complicating details of that case, and turned Galileo into a sort of martyr for science, victimised by religion. They then declared, with no evidence at all, that these two figures (Galileo and Darwin) were typical of
all interaction between science and religion. Of course the claim is ludicrous when you spell it out like that. Even if the analysis of the Galileo and Darwin cases had been accurate, you can hardly draw a conclusion about thousands of years of history from just two incidents! Modern historians reject the entire account - both the analysis of the individual cases which provided its "evidence", and the general conclusion about eternal antagonism.
Naturally they would rationalize it this way.
Ah yes, "rationalise", that's another word like "technicality". It means "I'm going to ignore the actual reason why someone did something, because I prefer the reasons that I think they should have had!" Seriously, if you think it was just "rationalisation" then you should say why. You can't just
assume that the given reasons are dishonest. Besides, it doesn't make sense to call it a "rationalisation" in this case. The theory behind the orthodox/heretical distinction was laid down in the second century. The actual attempt to
physically suppress "heretics" didn't really begin until the Middle Ages, centuries later. So I don't really see how the former can be dismissed as a "rationalisation" of the latter. On the contrary, isn't it more reasonable to see the latter as, in large part, a natural development from the former?