I can see the anti-homosexual mataphor in there but I don't think it's specifically a metaphor about that but more about simply outcasting people for "being different" period. I mean I was outcast in school, not allowed by to the cool kids to play with them and all that simply because I was smart and wore glasses. So I saw a lot of myself in Rudolph.
So it's not a metaphor about homosexuality so much as it's a metaphor for "don't out cast people who're different because you never know what they are capable of."
I do find it interesting his peers didn't like Rudolph until they were shown Rudolph could do something for them. So it was less, "hey, Rudolph is a good guy and we should feel bad for outcasting him!" and more "hey this freak can do things for us!"
And why were Santa's reindeer such dicks anyway?