Part of the CF specification requires each CF card to implement an IDE interface. So no, there won't be any problems, because to the computer, the CF card looks just like an IDE disk.
Of course, most CF cards only implement PIO modes (at least these days, you usually get some of the higher PIO modes). And yes, you only get a limited number of write cycles --- but that limited number is reasonably high these days (some manufacturers guarantee up to 100,000 cycles).
