Do Not Run Advertisements on Charity Streams
Twitch has stated time and time again that they do not make money from charity streams. While this is technically true insofar as donations using the tool are concerned, from my reading of the FAQ, they still make money from their cut of subscription fees, bit sales, and advertisements run during charity streams.
While bit sale profits are hard to manage because of its nature as a currency that can be bought at any time from any or no channel, and subscriptions may be hard from a logistics standpoint to funnel Twitch's take to the charity, there is an easy way to remove advertising revenue: Do not run advertisements on streams marked for charity.
Any streams for a charity, with this system, would have all pre-roll, scheduled, and manual advertisement runs disabled for the duration of the charity stream event. This way, we can be sure of the transparency of Twitch in matters of charity streams. As long as Twitch gains advertising revenue from charity streams, the altruistic nature of the service is called into question.
As an additional benefit, an ad-free experience would encourage more viewers to watch charity streams, and therefore donate, ensuring more money goes into the hands of the charities sponsored.