I don't think there are many good options because the tool is so restrictive.
Per the docs:
"... update does not delete artifacts that are not described in the current definition file. It can add new checkpoints to activities, but cannot drop checkpoints from deployed activities. The update can neither rename checkpoints nor change checkpoint
Once an activity has been deployed, the actions you can take on an activity become restricted. Specifically, you cannot delete items from an activity unless you are prepared to have your administrator undeploy the entire BAM activity and view sets and then
redeploy them. This can cause an interruption of visibility and loss of data
unless the administrator does a backup and restore of the data.
You cannot use this command to add new activities to an existing view. To add a view to an activity you must create a new view that includes the new activity. You can then undeploy the old view, but be aware that you will then lose your OLAP data history."
So some restrictions are hard and there is probably no way around them. It sounds like you can delete an item from an activity and keep the data through a backup/restore, but what a pain! The documentation around BAM is so poor that few
people have much knowledge of how the update process works.