Actually, the lavae will pupate even if unseparated. The thing is, it takes time. Zoophobas are pretty long lived. I had a bunch of them in peat moss for a while. I ignored them for a good 6-9 months (aside from feeding them), as there were only a few dozen in there. When I was cleaning things out, I found some beetles, pupae and big worms. HUGE ones. Some were 3" long and very fat.
If separated when small, they just go ahead and pupate - this is what I always do when breeding them.
However, if just left to feed and go about their business, they'll eventually pupate.
Most chameleons spit the beetles out - they smell bad and taste far worse - (it was an accident, trust me). They can be washed. I wash their rear ends off, and the chameleons love them. Especially my melleri. They like mealworm beetles too.
A bit of chitin isn't bad for them. I imagine it's good for them in moderation. Like fiber. They have some limited ability to digest chitin, as the shells of these beetles are partially digested when passed. In the wild, much of their diet consists of very crunchy insects - they're not going to eat many soft-bodied ground dwellers and grubs in their native habitats.