You can mute the node to disable it.

import bpy
scene = bpy.context.scene
compositing_node_tree = scene.node_tree
compositing_node_tree.nodes['File Output'].mute = True

You can set the mute flag of the Node to True.

import bpy 

scene = bpy.context.scene
compositing_node_tree = scene.node_tree
compositing_node_tree.nodes['File Output'].mute = True

Alternatively you can just call the bpy.ops.node.mute_toggle() operator within the compositor.