Assuming you want a 50%/50% square wave output I would just load up the MStimer2 library and have it's ISR just flip the output pin each time it's called. So I would just set the timer to interrupt at the millisecond value that corresponds to one half the period time of the desired frequency you wish to use. To change the frequency just
stop the timer interrupt, issue a new set timer interrupt with the new time value then do another start timer interrupts. Simple and low overhead I would think?
http://www.pjrc.com/teensy/td_libs_MsTimer2.html
Lefty