Depending on exactly what you mean by 'run', you could put in a constraint upstream of the stages you want to 'shut off' that ensures no rows pass that point. The stages would still run but they would process zero records.
-craig
"You can never have too many knives" -- Logan Nine Fingers
Occasionally we will develop jobs that have a reporting component and various inserts into our database. We will create an environment variable "Insert Data" and default that to no. When the job is run with the Insert Data variable set to no only the reports are generated. When the job is ran with the Insert Data variable set to yes the reports are generated and the inserts are made. This is implemented with a constraint in a transformer. You may be able to use this type of technique to limit which stages are executed.