if your Area2D is the base node of the player, you should have something like
as it is discriped in the Godot documentation.
Here you can move the sprite and the collision shape up by spriteHeight/2. This way your Area2D.position is located in the bottom/center of your sprite and collision shape, and the scalling is happing towards this point.
You can set the position manuelle in die sprite and the collision shape or by script in the _ready function, like
$Sprite.position.y = -1 * ($Sprite.texture.get_height()/2)
$CollisionShape2D.position.y = -1 * ($Sprite.texture.get_height()/2)