I can answer your question, hopefully enough to satisfy.
First off, I am a Ph.D. in the faculty of Medicine at the University of Toronto. So I do know more about research than the average person.
1. With regards to research with animals, there are few limits as to what the scientific community would criticize just general research, let alone an important breakthrough.
2. Most ethical questions come into play when 'humans' are involved. i.e. stem cell research and human testing. Many of these issues are currently dealt with by the law.
Many of the people that make the laws have no understanding of the science involved.
As to whether a breakthrough would change people's minds about 'unethical' testing/research.... This is where we see the hypocrisy of humans. This really boils down to the individual. I'm sure there are lots of vegetarians out there that are against the cruelty of animals, but would not think twice of taking advantage of medication or immunizations that came at the expense of years of animal testing. In this sense, I think it is like war. If a country went to war, but it turned out that that war saved an entire country from the brink of destruction, then I'm sure a lot of people would overlook the means to save the country, but it will forever be in debate.
Personally, I would say that science does question the ethics or methods of research if something bad happens. For example, the design of polio vaccines. It is widely argued that certain methods used to create a polio vaccine back in Congo, led to the emergence of HIV (or AIDS). This had less to do with the ethics of animal use, but more about the ethics of scientific procedure (whether proceeding or not even though you are aware of dire consequences.)
There are ethicists in science and that is their full time job. I never did take an ethics course, so I cannot help you beyond this, unless you have more specific science related questions.