Really, your question just illustrates the fact that this debate is entirely subjective and based on emotion.
As a further thought experiment, we're obviously already working on growing human organs for the purpose of organ transplants. Would people be ok with growing individual human organs for the purpose of food? I expect most people would think that would be gross and be against it, but ethically it seems in the clear.
The argument against this has nothing to do with Eloi thoughts and feelings, and everything to do with their ability to invade the Morlock tunnels and wipe them all out, as a matter of survival. That is, it doesn't matter if the Eloi object, if they lack the means to enforce their objections. Eloi thoughts do not carry any weight in Morlock arguments.
Besides that, feeding themselves to humans by the billions as captive domesticated prey species may be the only shot those species have at reaching other planets.