Yeah, Geostigma is basically Jenova's post-mortem attempt to continue corrupting and harming the planet's own life. Just as Kadaj, Yazoo and Loz are manifestations of Sephiroth's fragmented spirit, Geostigma is the scattered remains of Jenova's spirit. By gathering all the corrupted spirit energy from Geostigma's victims, Sephiroth was going to exert new control over the planet - to choke and corrode the lifestream, as he described it.

Aerith could've tried to cure it earlier, possibly - but with active remnants like Kadaj still running around, the change might only be temporary. Treating a symptom, rather than the cause. That's my theory, anyway. Removing Cloud's stigma gave him added strength and a more stable hold over the Jenova powers within him, but until he beat beat Sephiroth again he - and the other Geostigma victims - wouldn't truly be free.