If someone were to start an organization to rate merchants and certify them as a trusted crypto currency business based on clear publicly stated criteria would you as a business be interested in providing potential customers with peace of mind and would you as a consumer be more likely to do business with someone that has been vetted by an impartial and transparent organization?
The problem with your proposal is that most of the entities that lost/stole customer funds would rate out as trustworthy right up until when they're not.
IMHO the correct solution will be advances in the technology and, in some cases, regulation. i.e. greater decentralisation, multi-sig, things like that.
Existing established businesses that have been selling things online for years and only recently started also selling things for bitcoins do not really suffer from these problems. It's very new bedroom currency exchanges — written in PHP by people who should not be trusted to operate blogs about cats — that are getting exploited left right and centre.