One would think that someone as innovative as Santa could recognize that different talents are necessary to keep a business moving forward. In this day and age, you can't stay competitive with such a backward attitude. While it is clear that Rudolph's nearest associates learn their lesson by the end of this cautionary tale, the revelation comes mainly from guilt and necessity and not true acceptance. One has to wonder if the next reindeer born with a third eye or blue hooves will meet a similar fate if they cannot prove their economic worth.
While societal cohesion and sameness has arguably played its evolutionary role in advancing the species, even primitive societies often venerated those who were different as shaman or priests. And while Rudolph's "red nose," so shiny that one "could even say it glows" could possibly been seen as a birth defect worthy of ostracism from the gene pool, in the cultural environment of Christmas Town, where survival clearly does not depend solely upon passing on desirable genetic traits, is it necessary that he be turned out from the herd?
In the end, it's Rudolph's contribution to the productivity of the enterprise that gains him acceptance and a place in the community.
It's a fun if often infuriating story, much enlivened by the secondary characters of Yukon Cornelius and the oddball population of the Island of Misfit Toys. It should be noted that the happy ending, which awaits the viewer, also includes the symbolic castration of wilderness through the literal de-fanging of a menacing species, giving the most annoying character, the aspiring dentist, his place in society.