I agree with your correspondent that it would not be good for Turkey to be run by the generals, and I also agree they are prone to some wacky conspiracy theories. The issue of Turkish conspiracy theories was handled nicely by Sedat Ergin, one of Turkey’s top journalists and editors, here. But, you’re making a straw-man dichotomy. When previous governments have pushed the bounds of constitutionality, the generals have pressured for constitutional enforcement – but, 1960 and 1980 excepted, they have not taken control.
People forget that the Turkish courts did find the AKP guilty of violating the constitution back in 2008, but split on the penalty (allegedly after a hefty bribe to the deciding justice). The AKP is not a monolith, and plenty of more moderate and more law-abiding officials were ready to take the helm. They would have been nationalistic, and they would have listened to the Anatolian constituency, but they would not have subscribed to its lunatic fringe.
One quick fix is to strip Turkish parliamentarians and the prime minister of their legal immunity. Erdogan, Kemal Unakitan, and others have had numerous corruption charges delayed simply by nature of holding office. Accountability of Turkish politicians to the law would be a good start. It would also undercut the effectiveness of whipping up the anti-Jewish, anti-Alevi, anti-Freemason, and anti-Kurdish demons that Turkish politicians traditionally rely upon when they want to shift domestic focus away from their own failings.