First, I don't think IBM introduced Jython until WebSphere version 5.1. If you're running 5.0, you'll need to use JACL.
I don't have access to a version 5.1 WebSphere installation, so I can't verify my answer. In your own installation look for AdminTask.modifyWMQQueue. An excerpted wsadmin output from a version 7.0 install:
wsadmin>print AdminTask.help('modifyWMQQueue')
WASX8006I: Detailed help for command: modifyWMQQueue
Description: Modifies the properties of the WMQ Queue provided to the command.
*Target object: The WMQ Queue object to modify.
Arguments:
ccsid - The coded character set identifier.
...
qmgr - The queue manager on which the WMQ queue resides.
queueName - The name of the WebSphere MQ queue that will be used to store
messages for the WMQ JMS queue type destination definition.
...
Be warned though. In the past we have used Jython to manipulate data sources only to find out a recycle of the JVM is still necessary. I can't say that we've tried this with MQ.