There is conflicting information in regards to the location of Eagleton. In season two, Leslie (Amy Poehler) states that Eagleton is "two towns over." However, later on, there is a "Pawnee/Eagleton border," meaning the towns are next to each other, some Pawnee citizens having left and settled Eagleton.
Indianapolis is less than 3 hours traveling time from all of the major cities in the state of Indiana. Since Pawnee is clearly large enough to have a Parks and Recreation department, as well as its own television station, it is clearly a major Indiana city and thus should be closer to the state capital.
Sadly, most of Indiana's Native American population was deceased prior to the American Civil War. The Pawnee related troubles with its Native population wouldn't have occurred when the program relates to have done so.
Even if Pawnee went bankrupt there would be no precedent for the state to take over the city beyond its finances. Chris Tragaer could certainly direct its financial operations; however only elected officials could run the city and make the legal decisions for it.