My last answer wasn't clear, so although I am loath to rewrite answers that have been voted on already, I'll try to make this a bit clearer.
The Talmud has two opinions as to why bee honey is Kosher. Only one of them relies on the way in which bees make honey. The other says it is a "gezeras hakasuv" - an arbitrary distinction made in the Torah - which would mean it would be permitted even if it was an excretion from the bee like milk is from a cow.
The identification of the bee enzymes involved in honey production does not fundamentally alter the understanding of how honey was made. It obviously wasn't the pure nectar, even 2000 years ago, as only bees made it into honey. In fact, according to the opinion that bee honey is kosher because of the way bees produce it, shellac would also be Kosher (according to Rav Moshe Feinstein, at least).
The principle that excretions from a non-Kosher animal are themselves non-Kosher is limited by two concepts: "Pirsha Balma" - that what is excreted is not food, essentially. Bees wax may fall into that category, but the classic example is urine, I believe.
A more extensive treatment of the subject can be found here, which specifically discusses the enzymes of the cow stomach used for Rennet being different than the actual flesh. So even according to the opinion that it is the way the bee processes honey that renders it kosher, the fact that an enzyme from the bee is involved in the process does not change the conclusion. In fact, it is unlikely that it even changes the understanding from the Talmud, it just gives it more specificity and detail to identify and name specific enzymes and their function.