We have no way of knowing what other unshackled Reapers would do, because we have no other instances of there being an uncontrolled Reaper. But since we know each Reaper was once a species that was harvested by other Reapers to be created into a new Reaper (i.e., "preserving the species"), there's also no reason for us to automatically assume that most Reapers, if uncontrolled by the Catalyst and able to act upon free will once again, would choose to perpetuate an organics versus synthetics cycle. This possibility is enough for me to call "bullshit" on the Catalyst's blind belief that organics and synthetics will always want to destroy one another.
I'm not saying the Catalyst is right. I'm saying he BELIEVES he is right with as much certainty as, say, the Salarian Dalartrass believed that the resurgent Krogen would butcher the galaxy, or earlier, that Wrex believed the Rachni would rise up again and menace the entire galaxy. It's an educated assumption based on past experiences, but depending on the circumstances that assumption may have varying degrees of accuracy.
At the end of the day, though, what the Catalyst believes need not have anything to do with what actually is. Even if he doesn't know what the hell he's talking about -- which he doesn't -- he's still holding all the cards, and he's really just one last hoop that needs to be jumped through in order to resolve the conflict.
Speaking of bullshit, did anyone else roll their eyes at the Catalyst's expanded description of Synthesis? It says that it had tried similar solutions in the past, but theorized each attempt had failed because the outcome had been forced upon the species in question. It says that Shepard can make the choice - except that Shepard is then acting in the Catalyst's stead, and still forcing that outcome on the species of this cycle. There's no difference.
Again, the simpler explanation is that the Catalyst has NO IDEA why Synthesis failed before and has only a vague understanding of how this entire process is going to work. The only thing for sure is that the Catalyst would prefer not to have the reapers destroyed, but for whatever reason he can't really control them (he can only sort of redirect their focus in a specific direction) nor can he trigger synthesis on his own. The most obvious reason for this is that the Catalyst is actually a projection of one of the Reapers -- probably Harbinger -- and can't use the Crucible to affect the Reapers for the same reason a human being can't safely incubate the plague: it would begin to affect him LONG before it could affect anyone else and then the circuit would be broken.