Funny that you bring up Bowie, you're actually helping my argument. Sam Bowie had an injury in college that prevented him from playing two seasons at Kentucky. Portland ignored this red flag and drafted him anyways...the end result wasn't good for Portland. Embiid has been diagnosed with a spinal stress fracture...not an injury that NBA teams should be taking lightly (especially for a big man). The Jazz could take the Portland route, ignore the warning signs and draft Embiid. For the purposes of this particular discussion, if the Jazz had picks #1 and #2, I'd take the two best players available that also filled a need (and don't have a history of injury problems)...that would be Wiggins and Parker.
Food for thought: The last time the Jazz drafted a big man with a history of injuries in college was Curtis Bordchart...do you remember how that one turned out?