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)