You could do the PWM control on the capture registers of Timer1. Use it for both your interrupt and PWM. You would have to do the code yourself though.
I have not tried this myself but maybe you could use the capture register to set the PWM output then clear it in your ISR. You calculate the correct count value to set the PWM output and load that into the capture compare register.
Software PWM using your timer1 interrupt. This might not be practical unless you can get away with low frequency PWM or low resolution in the number of available percentage steps.
Another option might be to simple enable the overflow interrupt and let the Arduino lib control the timer. I have not studied the code but I suspect that the timeout interval setup by the library is fixed and may not be too fast for you to deal with. This way you might continue to use the built in PWM functions.
Maybe someone else stumbles upon this, so I'll answer my own question: with no specific settings it is possible to use INT0, Timer1 and the three PWM outputs 5, 6 and 11.