Do Arduino Due' timers give us only low frequencies?!

From my experience with Industrial Steppers you won't be able to get more than about 1kHz with just a voltage drive. You would need to get a fairly expensive driver to go 5kHz or so. Add to that, most steppers are 200 Steps per revolution, so your speed would be about 5 revs/sec or 300 RPM. Remember you have to establish current in a fairly large inductance for every step. If you had an oscilloscope, you could examine how many milliseconds it takes to establish current by measuring across a low-ohm resistor. The voltage will definitely "lead" the current in any inductor. The times are very motor and drive dependent.