I would really, really, really love a Battlefleet Gothic - or, given the FFG licenses Battlefleet Koronus - version.
In some ways, the latter would be better; you needn't tread on the named ships like the planet killer or blackstone fortresses to be awesome - a rogue trader dynasties fleet of a dozen frigates and merchantmen can be a very characterful force, but you have room for the Navy, with actual line warships, or Karrad Vall's chaos raiders, the Undred-Undred Teef Orks, or the Rak'Gol.
It's also a setting with relatively limited fighter/torpedo proportions, meaning that you can make those very much 'special' counters rather than a core mechanic. Equally - unless you're the Winterscales - grand cruisers and battleships don't show up much, so you have 'space' in the scope of mechanics to fit plenty of distinction between transports and raiders, light cruisers and cruisers, and to have plenty of 'named' ships like the Fel Hand as well as generic equivalents - which keeps the character-centric nature of the game. It makes sense just about every battle that the Blitz Dynasty fights includes Jeremiah Blitz' flagship because he doesn't have many warships; Battlefleet Koronus itself only has about three or four line cruisers.
I would still leave pinning in - it's a key bit of making discwars work - but make it a combination of boarding and close-range broadsides (as rolling macrobattery fire forces a ship to divert power to shields, does lots of light damage, etc). Either way, it's going to be very much an orky/rak'gol tactic.
As with cards, discwars can afford to be slightly narrative and abstract compared to a 'normal' wargame.
Also, having pinning be boarding makes for some obvious mechanics - an assault boat squadron might be a cheap, fast, broadly useless disc - but flip it end-over-end up the board and pin some frigates with it; it'll put them out of action for a turn or two until they kill the bloody things, during which time you can manouvre to get the advantage.