I think one way to look at it is this: Do you really need all of those different skills? If no one but a magician is going to use pyromancy and hydromancy, then why bother having separate skills in a game that's more about simulation on a broad scale? Does it put too much of an emphasis on magic, or do you have to develop the same amount of game play around stealth and combat heroes? Sure, it's a great RPG idea that creates a lot of variety between characters, and makes each character unique. Is it really worth it in an RTS game, though?
This is a decision best made early in development, but it's a worthwhile one to consider, even if you're set on having a broad range of skills that characters can have.
Failing that, you should go with the option that keeps it as simple as possible while allowing the broadest range of choices. Here's how I'd do it without taking the myriad skills out: Have everything in that guild depend on the highest skill of the leader you choose near the beginning. This allows for some specialization and variety between games.
So, if you chose a mage who focused on having a high mana pool, he could make a College of Meditation. If you decide that you want to branch out into fire magic, you would need to train your leader so that he could master the necessary skills. This could be accomplished by leveling him up through adventuring or studying. Studying would require a significant investment to buy all the necessary books and tutoring expenses. You could summon mystical teachers (Costing more money), or you could go visit a master in a faraway land (Costing more time). In turn, the leader would train all of his underlings in the skills that he's learned. Perhaps not everyone will master the new skill, but in the least they'll learn enough to passably teach someone else should the mantle of leader ever fall on them.
This allows the player to choose an initial skill set for people trained at that place, but also allows them to branch out afterwards. Those who happen to be skilled in other magics that visit the Order will be trained in the new skill, and may be able to leave some of the knowledge of their own skills with the Order (Making it slightly easier/cheaper to develop new skill sets for your Order).
It'd be a little bit of work, but not nearly as extreme as getting rid of the skill or making it fully automated. The player just chooses the leader, what that leader learns, and then little thugs get pumped out into the meat grinder battlefield.