If they hadn't applied the same charges to legitimate 3rd party applications they could still do this and have avoided the massive community backlash.
Considering their horrible track record with advertising and selling Reddit premium this should be the single best way for them to finally monetize their platform. They didn't need to destroy what little credibility they had remaining to their users to get to this point, but for whatever reason they did.
Not only did they have the option, as I understand it the API was even configured as such since all requests from an app shared the same API key. They're basically whitelisting like this now but only for the accessibility oriented 3rd party apps.