I actually know that intersection (3rd/Pike) quite well and think the issue is more the 7/11, cigar shop, and major bus transfer point than the McDonalds in attracting loiterers/criminals.
I was wondering how it was possible for Macy's retail employees to work in the mall prior to Amazon's purchase, but how it was unsuitable for software engineers. Surely at one point the Macy's employees were selling fancy clothes, perfumes, and housewares from that location...