I couldn’t find the Guardian Story, but I was able to find this:
"We ingested the entire U.S. social graph,” Davidsen said in an interview with The Washington Post. “We would ask permission to basically scrape your profile, and also scrape your friends, basically anything that was available to scrape. We scraped it all."
That in a nutshell is the difference. They asked permission and it was clear the request was coming from the Obama campaign. Plus, you have the numerous criminal acts Cambridge admitted to on the videos including bribery, fraud, prostitution, blackmail and multiple election law violations including facilitating the illegal coordination between the Trump campaign and outside PACs. Overall, it is a rather poor attempt at false equivalency.
Furthmore, the Cambridge scrape in addition to scraping the user accounts that took the fake quiz scraped the entire accounts of all their friends. Obama was only able to scape the friend's list not the accutal account details from friend's accounts like Cambridge did. That is how Cambridge was able to get data on 50 million people.