No, overbuilding an opponent's Coal Mine or Iron Works is not allowed if there are still cubes left in the Market of the same type.

This is supported by the following rule:

• "If the tile you are replacing is owned by an opponent: • You may Overbuild only a Coal Mine or an Iron Works. • There must be no resource cubes on the entire board, including in its Market, of the same type as the Industry tile being replaced."
  (page 10)

Therefore, if there are still coal cubes in the Coal Market or iron cubes in the Iron Market, you cannot overbuild an opponent's Coal Mine or Iron Works.

Source: page 10

Source: Core Rulebook (pp. 10, 12, 8, 9)