I always thought they killed Sonny because he was unpredictable, which threatened business. By eliminating him, they, in a way, got a guarantee of getting Vito back with his level-headed judgement (not to mention political protection).

Sonny was always a threat to the stability the other families needed to profit from the drug trade.

And, as another poster had already mentioned, the worst case scenario would be that the Corleone family would self-destruct.