Your last sentence is what really needs to be worked on by people from both camps. A bridge needs built to reconciliate valid arguments from both camps, that is where the unifying process should take us and then the next step is to have one focused direction for all the muslims.
I have always been of the thought scientific discoveries and research needs moral checks, which comes through the proper understanding of Islam. An educated person in the midst of those sciences is more likely to bring balance to it by understanding the Islamic principles as compared to Islamic scholars bringing balance to it by understanding the scientific research. Some may disagree. However I have never found it difficult understanding the principles of Islam, which is why I make this statement. I find it very hard to envision religion in isolation from the world.