I went over the article with my rabbi who said it was relying on extremely machmir opinions ( and completely ignored the shulchan arukh) and that it is not the job of a rabbi to try to make something that is commonly accepted assur. He said we have enough actual problems and we don't need to create new ones. If chazal never wanted us to eat at a non certified kosher establishment they would have made those laws- instead they made bishul akum laws with all sorts of Rules and exceptions- they were not trying to make life impossible for us.
As long as you did ur research. It gets me upset when people say it's just coffee. It's not so simple to eat in a treif store that sells meat, the questions need to be asked.