The capital ships themselves are fine. They ougth to be powerfull, they ought to be used by the major factions to protect their interests. "Fairness" has nothing to do with this. But I don't think, there is real disagreement here.
The whole issue evolves around the "scoring method".
As long as the "the-last-bullet-scores-the-prize" rule was operative, the sheer capital ship's fire power made it unlikely to score this final hit. This rule was abandoned in order to make the game more fun for the player - which is a valid decision in its own right. However, this decision lead to the current situation, as it was not balanced towards those major help granted by capital ships (and, to a lesser extend, by system authority).
There was always this other request before the "Wings" update was launched: To implement shared bounties between players, where each payout would have been related to the damage inflicted to the target. The devs decided against it and did stick to the last-bullet-rule between palyers - which is fine, in my regards. (And "Wings" did change everything anyway...)
But MAYBE it is time to re-evaluate this decision. Not with regards to palyer/player interaction, but with regards to player/NPC battle outcome.
If the final combat bond/bounty would take the actual inflicted damage into account, "stealing" kills from a battle ship would still be easy - but way less profitable, as the capital ship would have done most part of the "work". But if the player would visit a "capital ship free" conflict zone and do all the fighting himself, his final yield would be way larger and adequate to his effort.
I think, this would be fair...