Outfitters usually use some of their user days for training trips, i believe, but it really doesn't matter. If 20 employees of a permitted outfitter choose to get together and run a private trip it, is not misuse of a private permit. Guides are people just like you and they have the right to go on private river trips if they draw a permit. Misuse occurs when someone profits off the permit. If the employees pulled a permit and then charged people more than the cost of the trip to go, that is misuse.
I've seen a few trips that I thought were true "pirate" operations, but I think they are rare. However, when I went back to college as an adult, it did catch my eye that college outdoor programs seem to regularly be using private permits. The school that I went to would advertise a raft trip around campus at prices 2 to 3 times what shared expense trips usually cost. After getting to know a couple of students involved with the outdoor program, they confirmed to me that work study employees of the outdoor program were paid to be on the trips and called themselves "guides".
I'm all for at-risk youth, wounded warriors, and the like going on river trips, but I don't think that 501c3 tax exempt status should be a ticket to pay yourself or your friends to take passengers on a private permit.