You can port the intake just as long as you leave it rough. Polishing disrupts atomization of air to fuel for side feed manifold engines. If the injectors were located at the top of the head (if it were direct injection) then there wouldn't be a problem with polishing the ports to the intake side.
I also want to make a note that to much porting will kill low rpm intake velocity which kills the streetable low end torque that most people like on there KA.. If you just want a high rpm engine you can increase port sizes pretty well and exceeded past 2mm. But if you are trying to keep it steetable and just want a little more kick in the mid and higher RPM ranges, without effecting the low end I wouldn't recomend anything more than a 1mm port increase from stock diameter.
Always remember to flow bench your work.
