Again, I just don't see where people have gotten the idea that Jenova is "permanently brain dead". It was incapacitated by some unknown Cetra magic, and then sealed by Shinra technology, only to be released and subsequently owned by Sephiroth. There are instances in Ff7 where we can clearly see that Jenova can recite a line or two of its own accord even though it is under Seph's rule. In AC it continues to be domineered by Sephiroth, but then he "dies"/is thwarted.
It seems as though it remains inactive during DoC, but all of a sudden Genesis wakes up because he thinks there's a problem he needs to fix.
I simply don't recall any material that says Jenova is done for and definitively shows that that there is no way it can ever become a threat in the future. The instinct of the creature as a whole exists in each of the individual cells, so as long as there are Jenova cells, Jenova will always be present. As long as it is present it will always be a threat to the planet.
Of course, if anyone's got material saying that Jenova will never rise again, or info to that beat, please provide.