The facts of the case (all canon, all presented in-game):
1) The reapers have killed trillions every 50,000 years for the last billion years.
2) Shepard is tasked by the Alliance with destroying the reapers.
3) Shepard has the approval/support of the Alliance and all the other known races to use the Crucible to destroy the reapers.
4) Neither the Alliance nor any of the other races has given Shepard permission or agreed to allow Shepard to take control of the reapers so if he chooses this option, he does so without their consent.
5) Neither the Alliance nor any of the other races has given Shepard permission or agreed to allow Shepard to somehow combine everyone with synthetics so if he chooses this option, he does so without their consent.
6) No one knows exactly what kind of creatures will be created with synthesis (will they still be able to have kids through sexual reproduction?, will the hybrids live forever? , will they share a hive mind or be individuals capable of independent thought and action, etc) but they will no longer be human or quarian or turian or asari, etc.
7) Choosing the destroy option kills all the reapers.
That's all I need to know to make the choice to destroy the reapers. No head-canon, no supposition, no guessing what might or might not happen in the future. It is the only logical choice that does not make use of supposition, guessing, etc.