There are two good reasons to trust the modern scientific community: one, because they use reality to settle their arguments. Human nature: some of these people can't stand each other, but in any case, those on opposite sides of a theoretical debate disparage the other side, believe their side is right, and they want to win. Reality is the thing they use, to beat the other side, to settle their disagreements. If one faction's argument can be overruled, the other faction is going to keep at it until it will be. The scientific community isn't a coterie of like-minded conspirators, getting their fake story straight in a back room so they can put one over on you. No, it's made up of faction vs. faction vs. faction, each with its own story of how things work, all working on the furthest-out reachable theories they can. They call each other and each other's theories wrong-headed, ill-considered, even crackpot! And eventually, reality is what settles their hash.
Controversy is largely limited to the cauldron of "active science": the area of theories whose predictions reach out further than what can currently be tested. While the practical scientists and engineers figure out ways to make the just-a-bit-out-of-reach theories testable, theoreticians continue to argue and refine their theories and predictions. Both sides look forward to what will eventually be experimentally confirmed, and every year, that's exactly what journals are filled with: controversies about new theories (that aren't yet entirely testable, or tested), and controversies about new experimental methods that have just been developed, and are being used to put past years' controversies to the test. The result that comes is an upset to the faction that believed the other thing, and you better believe they are going to scrutinize the results, and do it again. And do it again. And maybe even do it again.
But science eventually stops publishing do-overs. Science loses interest in deniers of reality, after reality has been proved by sufficiently conclusive and repeatable experiments. Active science is just a question of getting predictive theory into testable range.
Reality then wins every argument that science ever has. That's the first good reason to trust the modern scientific community.