Why are ecology and economics seemingly disjunct topics?
I think you are right to say that an economy is always a subsystem of a larger ecosystem, but it needs not always be modeled as such.

It may be interesting to have a precise and elaborate model of the solar system taken in isolation, independently of its interactions with the rest of the galaxy, other galaxies, etc. In very much the same way, there are many good reasons to build a model of an economic system without accounting for how it fits in a more general ecosystem. 

The same kind of question applies to many other topics. One could for instance ask "why partial equilibrium and not always general equilibrium?", "why small open economies instead of replicating the actual size structure of the global economy?", etc. I guess the only answer is that the smaller, less general models are considered useful in one way or another.

This is not to say that the opposite endeavours (the ecological economics attempts to model economic systems as part of an ecosystem) are worthless, quite the contrary. But there is only so much you can do and there is always a trade-off (in terms of estimability, tractability, additional assumptions, you name it ) to increasing the generality of a model.