There are two ways you could approach it - in your own mod delete the deployment then copy the standard TFTD deployment without the nextStage part:
alienDeployments:
- delete: STR_CARGO_SHIP_P1
- type: STR_CARGO_SHIP_P1
# copy everything from standard/xcom2 ruleset
# but either leave out or comment out nextStage
Or you can use the empty nextStage like this:
alienDeployments:
- type: STR_CARGO_SHIP_P1
nextStage: "" # when something in the ruleset asks for a single string ID, empty quotation marks is the proper syntax for not defined