It means that the military should follow (obey) civilian government for Democracy to function properly. Altering the order (military imposing government even if "democratic") violates the principle of Democracy. People should have the chance to argue, experiment and agree on political matters without the threat (fear) of military interference. The implication is that civil society thrives among people who don't need to panic over an imminent military dictatorship. In short, it is an indictment against military intervention in politics without a clear political consensus.
Gen Chiwenga's phrase, as implied by @Dan Bron, emerges from regional political history with a twist. It proceeds from a 1978 essay that attempted to explain and legitimize the separation of Eritrea from Ethiopia. The original phrase, "The important thing is not the gun but for politics to lead the gun," argued that the Ethiopian used of the military against civilians seeking independence in Eritrea was infringing on the principle of Democracy, and was an assault on good government. Chiwenga transferred it from a denunciation of proto-colonial expansion to the censure of military intrusion on civil society: from the context of national sovereignty (defense from outside threat) to national politics (domestic affairs).
I suppose that the phrase, in all its variations, would make implicit sense to people who have struggled with military elements meddling in civilian affairs. Chiwenga's recent use of it also hints at the influence of historical documents in the current African political discourse.