+1 to repechage. I see no harm in trying to create a new flat for the removal tool. Probably couldn't hurt to squirt some penetrating oil onto the threads from the back as well. If that fails, you can always then move on dismantling the FW.
By the way, what type of freewheel tool are you using? If it's one of the older, non-splined Regina freewheels, you might get a better purchase on the faces using one of these FW tools with a lip.
(Btw, I am going to be in San Jose tomorrow, and could let you borrow mine if necessary. PM me if interested.)