Should input/prometheus go away as well?

yes. actually we should probably grep around a bit more too. there might be some documentation talking about prometheus too, that we should clean up. and config files that may have settings about the prometheus input or query endpoint
do you mind continuing this ?
if you remove code, be sure to run ./scripts/qa/vendor.sh and if needed dep ensure to clean up dependencies.

Think this is good to go aside from a changelog update

looks great @fitzoh . unfortunately i can't approve this PR because it's my own :)