I have to say: when I didn't like the 4 way joystick extension that was provided by a 3rd party, I built my own using maths. It was pretty difficult, but the complicated bit was the coding blocks, and Stencyl did a pretty good job of teaching me that.
Although it would be pretty difficult to recreate Box 2D physics entirely within stencyl, the fact is that recreating certain parts of it (whatever part is necessary for your specific situation) doesn't have to be. Next time I'm going to consider it.
It is a shame that Box 2D in general doesn't have as good a performance as it might be able to. I'm interested to see if the anti-jittering patch makes a big difference to my performance or not. I'll try tonight.