Here are some of the things I came up with.
The unscannable 40 000m3 corporate hangar: Nothing within this hangar will appear to potential gankers when they scan your cargohold making it ideal for those high-value/ low volume items. Furthermore, everything in the corporate hangar is destroyed when you pop the Orca so nothing drops for those dirty pirates. Thus you are relatively safe from being ganked for profit... being ganked for pleasure is completely random and cannot be predicted or explained... a real life equivalent would be 11 beetle drivers pummeling into your shiny new BMW just to see the reaction on your face and the coffee stain on your $5000 Armani suit.
The ability to fit modules: Orcas have a 3-4-2 hi-mid-low setup for your fitting pleasure. Freighters cannot be fitted with anything. This gives you some versatility in that you can fit for agility, cargo capacity, etc. (although it does make your ship slightly more gank friendly in that these could be part of the loot from your wreckage).
Cheaper: Correct me if I'm wrong but the freighter comes in at 0.75 billion mark whilst the Orca is roughly half that value.
Total capacity: Orcas have a corp hangar of 40 000m3, a maintenance bay of 400 000m3, an ore bay capacity of 50 000m3 and a cargohold of 30 000m3. This brings total space to around the 500 000 - 550 000m3 mark. Most freighters carry around the 750 000m3 mark. So the Orca loses out here... in addition the different bays have restrictions as to what you can put into them (ie: unprocessed ore in the ore bay, ships in maintenance, etc.) so you can't even use the total capacity to your liking.
Total EHP: Total EHP comes in around the 60 000 - 65 000 mark, a freighter carries a 100 000+ total EHP. This makes the Orca easier to pop... BUT given the fact that you are less likely to be popped for profit this aspect is a bit of a misnomer. But it does make any attempt to gank a freighter an excersize in mass co-ordination (requiring in the region of 15-25 battleships to pull off successfully).
Skills: The Orca requires Industrial Command Ships I, Spaceship Command V, Mining Barge V, Astrogeology III, Science IV, Mining IV, Industry V, Mining Director I, Leadership I, Mining Foreman V and Mind-Numbing Patience V. This is a significant skills investment compared to the Advanced Spacedhip Command I, Spaceship Command V, Racial Freighter I, Racial Industrial 5, Racial Frigate III needed for a freighter.
Overall conclusion: The Orca has its place, especially when hauling high value items that are low on space (ie: implants). But the lack of overall capacity, tank and intensive skill requirements makes it more of a luxury in a hauler's hangar, with the freighter carrying out the day-to-day warp-and-grind bread-and-nano-paste jobs.
EDIT I: Removed jet canning from advantages as I was wrong... lol.
EDIT II: Attempted to fix various spelling errors and to infuse some comic relief... failed at both