Per Wikipedia, Pierre, South Dakota was "founded in 1880 on the Missouri River opposite Fort Pierre".
While the history of the name of the city is not mentioned, it's reasonable to draw the conclusion that it has something to do with the nearby fort.
Again, according to Wikipedia, Fort Pierre "derives its name from Pierre Chouteau, Jr., a fur trader who established the fort."
While no date is listed for when the fort was founded, it's a reasonable assumption that it was prior to 1880, as Pierre Chouteau, Jr. died in 1865. It's highly unlikely he founded the fort as a zombie, but Wikipedia made no mention of this one way or the other.
In summary, it's reasonable to conclude that Pierre, SD was, in fact, named after "some French Guy". (Although technically, he was American, but of French descent.)
I happen to think that the pronunciation of "Peer" comes from our lazy American tongues bastardizing it over time. However, this is based off nothing more than personal conjecture.