The Gunship can be used in groups in an anti-capital ship role, as small things are hard to hit in big things. Capital ship turrets will not do well against bounty hunter gunships, as they are small and agile. on their own, they can't do much to other capital ships/other gunboats. However, in groups and supporting bombers/capital ships, they can be used effectively. So I don't think they're overpowered in terms of anti cap combat, just that they are effective in group situations.
The Order Carrier has its advantages and disadvantages. It would likely perform well against other cruisers, battlecruisers and larger gunboats. However, as Tenacity has pointed out, it does not do well against battleships and small stuff. The fact it can't deal with anti-cap gunships is due to the major size difference - I'm sure smaller cruisers would crush them pretty easily.