NO
I think that is one of the strengths (design wise) of this mod as the number of minor arrays you destroy directly impacts the difficulty of the major array fight.
So.... if you think you can handle a massive space battle then you don't need to destroy any minor arrays. <- I did that after I completed the final mission and it was a good fight, clearing the last two major arrays at full strength. But I had upgraded three of the Cyberamps to Tier 3; so I was rocking 15% faster repair, 15% increased shield along with 15% increased ship speed. My fleet ships also had 15% to shields and speed. During one battle, just one of my fleet ships dropped to about half hull. The other three were fine.