The tuna, pidgeon, horse, drosophila fly, rat and yeast all have different biochemical pathways from each other, and yet all of these pathways use cytochrome C at some time or another.
Well no, since all the organisms you listed are eukaryotes they all use cytochrome C in exactly the same biochemical pathway i.e. in the electron transport chain following the Kreb's cycle. Since they are involved in an essential pathway they should be highly conserved, yet as others have pointed out we see the genes have acquired mutations in a pattern that conforms to the ToE's predicted nested hierarchy.
Your argument seems to be that the difference is a result of alternative splicing to get different proteins or RNA interference. However, the alternative splicing arises from the excision of introns from transcribed mRNA and this can give rise to multiple proteins from a single gene. However none of the cytochrome C subunit genes have introns so this would not be an issue. As for RNA interference, as far as I'm aware such sequences in the genome would not give rise to functional proteins, and besides this would only affect how genes are expressed, not their sequence, although I could be wrong as it's a bit beyond what I learned at uni. I'd also question that this was all an effort to make reduce the DNA required for the storage of protein coding sequences, given that half our genome is repetitive retrotransposon sequences.