How many times do we have to outline stuff shugenja could do that isn't blessing the mother-flipping crops?
The only thing that's needed to solve the "shugenja outshine bushi and courtiers" problem is to treat the religious and spiritual aspects of Rokugan as more than just window dressing. Make those things important, and hey presto, you have a sphere where shugenja can be the leaders, and stuff for their magic to do that isn't bushi-ing or courtier-ing via kami.
As I said, unless you want to add a third tier of things for Bushi and Courtiers to try and buy into, religous/spiritual events are exclusive to Shugenja. A Courtier can pick up a few ranks of weapon skills, A Bushi can take up an art skill and a few ranks of etiquette.
4th Edition has a LOT of info on the spiritual aspects of Rokugan, in fact it also has a boat load of spells that interact with the spirits and ghosts, etc.
Guess what, GM's usually ignore that, why? Because unless its a specific campaign, every other player will just yawn.