According to Domino 8 for System i Help (Help/i400help.nsf) Server 
Controller IS supported.
From the help:
To start a Domino server and the Java Server Controller using iSeries 
Navigator, follow these steps:
Note  You must have *JOBCTL special authority to perform this task.
  1.    Start iSeries Navigator.
  2.    Open the system where you installed Domino.
  3.    Click Network.
  4.    Click Servers.
  5.    Click Domino.
  6.    Right-click the Domino server and select Start -> Server and 
Controller.
Note  To start all Domino servers and Java Server Controllers on the 
system, right-click Domino and select Start -> All Servers and Controllers
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