Looking for a tool for creating or editing file and folder bookmarks (finder aliases)
Rather than attempting to edit an alias directly, you could look at making a tool that creates the alias for the user.

Using Automator you could create an application that uses the following built in actions:


Ask for Text
Connect to Servers
New Aliases


And when the app is run, the following would happen:


The user would be asked for the server address (you could pre-populate a default answer for this).
The share point would be mounted. A dialog would pop up asking for the users login credentials, which could then be stored in the keychain (more secure than having these details contained within the tool itself).
An alias would be created at a specified location, e.g. the Desktop.


You would then save this as an application and share it with your users.