I just wanted to say that I really like this idea. It is similar to what I was thinking about doing in E6. I might have to do a blend now.
I don't think there is really a major flaw here at all. From what I understood you were talking about more subtle (though large in scale) manipulation of plants and weather, Umbran is talking about combat spells. The ability to influence when the rains come is very different than blasting people with lightning.
Also what Wik said is helpful. Religions and cults can spring up for many reasons. Perhaps the dryad is just a dryad, but the local human population has built a mythology around her. Perhaps she uses this to her advantage, perhaps she ignores it, perhaps she tries to deny it (since when do facts get in the way of a good cult?) There are many ways to approach this.
I do agree however, you have to be very careful what powers you give these creatures if you don't want their CR increased. Making sure the added powers aren't combat oriented and/or quick to use is a good start.