No need. The M5 computer was capable of running a starship back in the day (TOS: The Ultimate Computer). Granted, it occasionally went insane and tried to kill everyone on your side (probably a Windows problem) but they've had 80 years to work out the bugs.
If that doesn't work, just staff each ship with robots. While Data is cutting-edge technology, surely it would be easy enough to make robots that aren't sentient but could perform their tasks adequately. Even if they aren't as efficient as humans, the sheer number of ships will overwhelm any enemy such as the Borg.
Better yet, take a Defiant class, eliminate the living spaces (or fill ‘em with more power plant, shields and weapons...), and turn ‘em into UCSVs (Unpiloted Combat Space Vehicles). Just a have a few command ships backing them up and the Borg (and the Klingons, and the Romulans, and the Cardassians and the Ferengi and the...) will never know what hit ‘em...
So I guess you'd advocate recompiling the source code to work on a Mac, then.
If that doesn't work, just staff each ship with robots. While Data is cutting-edge technology, surely it would be easy enough to make robots that aren't sentient but could perform their tasks adequately. Even if they aren't as efficient as humans, the sheer number of ships will overwhelm any enemy such as the Borg.
Why not? As long as you are willing to take certain chances:
(Remember, Data has an on/off switch)