The Pokémon Tower in Lavender Town has been replaced by a Radio Tower, similar to the one in Goldenrod City. In turn, the Pokémon grave sites were moved into the newly added Soul House.
So I guess Game Freak just wanted to add more to Lavender Town. They kept the Pokemon graves and moved them to the Soul House, so they weren't really taking away a key part of Lavender Town. It's just what Game Freak decided to do, there is no way to know for sure other than asking whoever did it.
Hope I helped! :)