I think if one were to attempt to kill another players species, they'd subtly influence their own species to directly or indirectly affect said creature through evolution. Like Termite's example with the large whale and the small fish. They'd adapt to have an appetite for larger creatures, sharper teeth, blade like dorsal fins, etc. Through that, they'd either over hunt them onto the verge of extinction or the entity retaliates by building up defenses. 

If I have any input (of course I do, it's just a matter of whether my input is relevant to the GM or not. QQ) I do like the idea of manipulating the environment, though I think the intended purpose of the RP is to focus on the evolutionary process and what certain deities would do if given limited control of species that aren't already maintained by other entities, of which they've no idea about. The throwing of my two cents. Nom nom. If I'd compare your idea to anything at all, I'd compare it to the entity you play in the Indie game 'From Dust' where you aren't allowed to directly affect the tribe you watch over, but you can indirectly do so by manipulating the surrounding area, be that the ground or the water, etc.

Of course, there should be some fine tuning done to be able to incorporate it well into the RP itself. Failsafes, etc. to keep from overly making a, pardon my French, douche of yourself by intentionally and continuously trolling another entity through the environment. @_@ I'm fine with introducing entropy into the mix (we have an entity designed for that), 'cause it'd be boring not to, it's just the overstepping part that can really be problematic. Everything needs guidelines to prevent from abuse.