Of course, it's possible.
You need to use the RCP toolkit and set eclipse.exe (or whichever your system binary is) as the AUT.
You don't want workspaces to collide: You can use the Jubula standalone or you need to run two instances of Eclipse. When you execute a Test Job, it will start the (or seek for a running) instance of the Eclipse. Thus you need two workspace folders; one for Jubula/Eclipse executing the tests, another for the Eclipse being tested.
You can use the Observation mode to detect the actions you perform. It's disadvantage is that this way your tests will be less reusable and harder to modify. If there's a change in the actions, then you better record the whole process again.
Or you can create your tests manually by adding Test Cases and controller mappings. This requires more practice/time.
If you don't want to spend much time with it then just use the Observation mode.