sounds like a beautiful place. the best way to slow down creek water (IMO) is to dig a sediment basin above yer pond (not to dam up the creek). give the water a place to slow down and drop its load before getting to yer pond.
could the "common minnows" be some kind of creek chub? if so, i wouldnt think they would cause any harm, and probably add some forage base.
aerating and feeding most definitely increases the carrying capacity, if managed well it would be many times that of an unmanaged pond.
i'll bump brettski's question....out here in CA its dam near impossible (ha) to change a creek if it hasnt been done already.