If Death Watch are happy to join the separatists that is good for the seperatists (one more system) - that might be seperate from the independent systems being considered a threat.
For example 'Seperatist System 42' might be looking at a costly war with The Republic and decide that they should break with the Seperatists and merely declare non-violent independance - the independant systems offer a model for how to be an independent system and possible a group they can join to have some protection, if The Republic accepts that then the entire seperatist movement is in doubt.