It was the common sentiment at the time, something I've seen from many people, including reports from the time. Everyone, probably including the Trail Blazers, saw Jordan as the better talent...but many, certainly including the Trail Blazers, felt Bowie would have more "impact" due to his size. Something I've also seen Blazers officials of the time say was that they were looking for the "next Bill Walton." Walton had set the blueprint within the organization for a great center: someone who could pass and shoot and run despite being a center, and Bowie fit that.
Bowie over Jordan was the common sentiment, just like Oden over Durant was. If you read that Jordan was the better player, I'll speculate on what the writer meant. Jordan had the best post-Wooden college coach, so he knew defense better than Bowie. It can always be written that the 6-7 guy is a better player than the 7-1 guy, because he usually has a bigger repertoire of abilities and moves. But obviously, premium big men are drafted before smaller players unless a difference is obvious, and it wasn't from what I read.
You say Jordan was the sure thing; it was the opposite. Jordan was the risk and Bowie was the sure thing. Jordan (2 years in college) had recently emerged on the scene while with Bowie (5 years in college due to injuries), I had seen articles since he was a high school junior. Jordan stuff had been in the media a couple of months since March Madness; Bowie stuff for 7 years.
I suppose a great genius could have selected better, but for scouts using the usual methods with their ordinary intellects, I don't fault the Blazers for choosing Bowie over Jordan or Oden over Durant.
As for a writer saying Jordan was better due to winning an NCAA championship, Jordan shared in the glory, but Dean Smith won it. Jordan was just one of several near-equals on that team, while Bowie clearly led his team. Bowie was more dominant that Jordan because Bowie led his team, while Jordan shared the spotlight with teammates like Sam Perkins, Brad Daugherty, Kenny Smith, and Joe Wolf. Perkins won more awards than Jordan.
The problem, of course, is that Walton was dominant in college and Bowie wasn't. Jordan was, as evidenced by the awards he won (two-time consensus first-team All American and four Player of the Year awards in the season before he went pro).
"Four Player of the Year awards" in one season simply means he was Player of the Year for one year, suddenly gaining notice. Jordan was AP player of the year once, but Bowie had been AP All-American for two years. As for consensus, Bowie was All-American in 1981 and 1984; Jordan in 1983 and 1984.
http://www.hickoksports.com/history/mbaskallams.shtml