Is possible to call the pydev refactor (passing a new/old class name) from a Java code, such as clicking in a button in an Eclipse plugin?
If you mean in an Eclipse plugin with a dependency on PyDev, then yes, it should be possible...
Take a look at the test-cases for this: com.python.pydev.refactoring.refactorer.refactorings.renamelocal.RenameClassRefactoringTest