I work for Lakota and went through their training last year as private kayaker and rafter looking to work on the river, and I can vouch as a regular, non-manager type guide that Lakota's is a great program, and great people. I also have met Brenda and Paul at CRG and see them and their crew on and around the river quite a bit, and they are always very friendly and courteous people.
As for paying for training, while this does suck for first year guides, it is sort of the nature of the beast. If you want to be a pilot for Delta, you can't just show up with no experience, expect them to get you your pilot's license for free, and then expect them to gaurantee employment. Same thing here. You have to get certified, it costs money to train you, and not everyone wants to work for the company they train with, or is able to. Gauranteeing employment would be a nightmare. Believe it or not, you can make it through guide school, and totally suck ass as a guide. The state requirements are that you receive a certain number of hours of training, but they don't require you to pass a test or anything. Each company wants to hire people that are good boatmen/women, they fit in with the other guides, and would work well with their particular customer base. I've never been to a job interview that gauranteers me a job. Like Brenda says, if you area already certified, it doesn't cost you anything to apply.
I think it is fair to have to pay, but would be nice if you were reimbursed some of it later, if you are hired and stick it out with your company for a season or two.
Anyways, most guide schools are going to require payment, or a deposit or something. If they don't, then they are probably expecting some kind of work commitment from you. For me, the $300 or whatever it cost was worth it- now I can work one of the coolest jobs out there! I would agree that you should talk to the people who own/manage the place you are going to train at, or want to work for. Go ask to talk about their program, and you will get a feel for if it is a place you want to work/train at.
Liquidchaos can give you all the info on Lakota if you decide to go that route.
Sorry for the rambling post, but I'm already getting excited for river season. Hopefully it will snow up here some in the high country before spring!