I have always taken it to be a song of equality among men, or at least something akin to that.

Lines like   

"You're a better man than I am, Gunga Din"

"An' for all 'is dirty 'ide
He was white, clear white, inside"

I think its more of a read between the lines thing, but I could be giving kipling too much credit.

I love the song and think its positive. Would I sing it in today's crazy world of political correctness? Hell no, especially not in Canada.