I want the money to go to the organizers directly
Then you should think of your implementation as a "service provdier only" that has Google Checkout "integrated" into your service. Your relationship is defined as such - while your customers - event organizers and their customers have their own relationship(s) with Google Checkout
This way you are not party to the transaction that occurs between them and Google Checkout.
Additionally, Google Checkout only pays out directly to the merchant (they don't have any other type of "disbursement" that I know of).
is this a better way to handle transactions instead of having just one merchant id (the website) and funnel the money through it and distribute to the organizers from the users, at the same time charging them for some extra fee
I think you already realize the pitfalls just by asking it - you realize that its not just a technical matter - you have your own liability to think about when you are party to the transaction(s).
- What would you do on a chargeback? It's your account that is "hit" by that...
- What would you do on a refund?
- What would you do when there is a dispute between event organizer and their customer?
In these sample cases, you will have to deal with all of them - your "users" are "irrelevant" to Google Checkout (they don't "exist" in Google's eyes).
Also, I'm no lawyer btw, but Google doesn't allow any "fee" that is somehow added to the transaction for use of Google Checkout, per their TOS.