I don't know the answers for all of these, but I think for the majority of them the answer is no. You could definitely build your own facilities since much of what you want to do can be done from an activity inside of the platform. You could set up some sort of listener to run the activity and return some sort of response. That said, for much of what you want, you're probably better off inside where you can see all the data and have validation to prevent incorrect values from being set, etc.
I have some thoughts on your specific questions...
1) Generally, you don't want to ever remove a user account. If someone shouldn't have access you should disable it and change the password, but removing it takes away a key piece of the audit trail and can potentially break items assigned to that user. While that stuff can be fixed, it introduces headaches.
2) You'll need the UI to work with flows. To do otherwise would involve with directly manipulating flow data internals and we make no guarantee that stuff won't change from version to version or hot fix to hot fix, so your code could cause some major problems down the line if/when things change.
3) The System Management Application (SMA) makes cycling services fairly easy.
4) You can look at things like status of the work object from the exposed column in the database. I'm not sure if a tool like SQLPlus is sufficiently command line enough for your needs.
There are a few things that you can from a terminal using Pega utilities. Check out the prUtils file, located in the install media at ~\scripts\utils . This works on both Windows and Linux and can do tasks like import and export rules or manage hotfixes. Mostly, though, Pega needs to be administered from the graphical interface. It's always possible to create a service that can receive commands and modify work based on that - a REST service that allows GET, POST, or DELETE commands, for example - but for the most part administration of users and work objects needs to be done using the graphical interface.