However, it will completely prevent the heater from working correctly. The coolant needs to flow through the core in a specific direction to properly absorb heat from the engine coolant and transfer it to the cabin air. Reversing the flow will mean the coolant won't pick up heat effectively, resulting in no, or very little, heat coming out of the vents.
So while it won't physically *hurt* the heater core, it will render your heater useless and is therefore a pointless and potentially frustrating exercise. Make sure you reconnect the hoses correctly as indicated by their original placement.