I think it boils down to what you consider an "analogy", is a markov model really an analogy between computer science and biology? I would consider that simply a mathematical concept that finds applications in both Computer Science and Biology, and it isn't even that related to computations or computers, it's just an useful mathematical tool. I don't deny concepts from CS or Mathematics can be applied to biology.

On the other hand, I think there are lots of CS people who apply blindly oversimplistic models to complex biological situations without understanding the biology, and that's what I was trying to protest against.