if you know what i have writen about the Bohrok you know that just like i wrote about Makuta, they too are not evil. They are more like Galactus who himself is not so much evil as he just do what he does to survive.
i think its better if the Bohrok are sentient, instead of being like their G1 counter parts, which were just as you said, a mindless swarm who knew only about destruction.
the only reason the G3 Bohrok would have a desier to eat all that was on an island is because they have to convert the materials on the islands into energy that fuels them, if they don't they will die and they have no wish to die.
its like with my consept for Makuta, they are not evil, but their actions make us see them as evil, but there is more to them than that.