If your system can guarantee that the actual activation takes place, the best way would be total isolation of the electronic systems. No network access, no open nodes, denial of all command systems on API and operating system levels.
Alternatively, don't use much computer technology and let the launch platform receive codes, start engines and charge capacitors, while at the same time destroying its control systems with a power surge. The projectiles would be released when the capacitors are ready to release the power stored automatically without any need for intervention.
This would also mean destruction of your launch platforms, and you wouldnt really need an engine either. As a variant of this, use your launch platform as the projectile.
The problem is, if you do either of these, you are also unable to stop a bombardment order if a rogue element had control, or if you want to abort a firing mission.
Not using autonomous systems isn't really a solution either, as people are necessarily a weakpoint. People have desires, they have a price. Nobody is the exception really, it does only depend on the price, and be it the life of your lover, brother or child.
My point is, regardless of which method you use to secure your platforms, you will never be able to remove all of their risk factors. You can manage your risks, by implementing protocols, redundancy, technical solutions and organizational solutions, i.e. accepting the risk as unavoidable and mitigating it by f.e. having enough platforms that losing a couple wont make a difference, or by having a sufficient anti-platform-weaponry at hand to destroy them before they can launch (which is then also vulnerable to a similar array of threats).
TL:DR You could say its similar to IT-Security. You can never be sure nothing is going to happen, in fact, it is guaranteed it will happen, and you can only minimize the damages this will cause.
My proposal would be to distribute the firepower as much as possible, so each platform only has minimal armament, thus accepting the risk of one getting hijacked, but being sure that losing one will not compromise most of your infrastructure.