From a roleplayer perspective: It's obvious that Inara (as a Charismatic Hero) has taken the Archaic Weapon Profiency and is thus proficient with bows and swords. But she lacks the Personal Firearms Profiency. Having an already meager attack bonus due to her chosen classses, she didn't want a -4 penalty to her attacks.
Still, it is correct that she is not the greatest asset in a fight (just as Kaylee isn't, judging from the series), at least not when you only count her weapon fire. I don't know if she used her Charismatic Hero Inspiration talents (assuming she actually took these talents, since as a Companion, the Charm/Favor route was probably more useful to her)...
In the movie, her special talents weren't needed much, though she managed to surprise the Operative with her makeshift explosives. The whole scene gave Mal finally some kind of warning on what was really going on...