...is that Isran will walk in, try to kill you and then engage Serana next as she joins the fight.

How do I get to beat Harkon as a werewolf and avoid that? Or at least make Isran stop.

Wait as soon as you can. You should turn back once the wait menu ends.

You'll be meeting your boss in your skivvies, but I guess that's preferable.

Isran should embrace the nature of the beast. natural vampire hunters right there heh.

But yeah as suggested as soon as Harkon dies, try to set the wait time ahead one hour. That should do the trick. Not sure if you'll miss any of Isran's crap or if he will still be there for dialog.