I fully expect him to launch a propaganda war against the WC featuring his usual heavy handed Star Wars metaphors.
For real, though, I expect him to found a new and competing institution of organized Wizardry, incorporating the low talents of the Paranet, and working closely with both Summer and Winter, and focusing on an aspect of balance, like the fae.
This means they wouldn't kill, but rather recruit and work to redeem kids who started the slide into black magic due to lack of guidance. This would allow Harry to begin to build the larger powerbase he refers to at the end of BG.
To balance Harry, and to liaise with Summer, this would involve pulling in Elaine. She is sort of a lighter mirror of Harry, so this would fit very well with the story so far.
The WC would definitely order Eb to kill Harry at this point. He will refuse, causing a schism and breaking the WC's power in the process. Because Jim is an asshole, he would then definitly send Ramirez to kill them both.