Minds are made within specific psychological parameters. While variation and natural development is allowed, a Mind that violates the Culture's norms so grossly is a once in forever event.
Apart from that, I think one of them did decide it would read minds without permission. I don't know what happened to it, but it probably isn't anything good.
EDIT: how this squares with free will and individual liberty? Eh, I don't know. But that's how it is.
Additionally, GSVs are the ships that can build everything. A GCU is not able to manufacture ships (or at least, they were never described to do so, but I don't doubt one might be able to, given enough time and effort). GSVs have multiple Minds (3, I believe) and while one may deviate, the others will overrule it.
The other thing is that the Culture currently has a moratorium on direct experimentation with the Warp. Which all the ships know to follow due to the exact nature of the threat you mention.
They're afraid of exactly that. A fleet of Chaos Culture ships coming to burn everything in the galaxy.