A Kafer Beta is well armored but it's certainly not an Alpha. An Alpha is so well armored it's not worth the time to shoot at them. The times I played that mission, I was pretty much always able to cripple the Beta (at worst) or destroy it with two Kennedy cruisers without taking a single hit (which is a good thing since Kennedy class cruisers have glass jaws). There's a case to be able for closing with the Kafers since their CQ is so awful for like half of the game, but it's so much safer to just exploit the lack of TTAs on Kafer vessels and pound them from afar. But then again, I always felt that GDW made the Kafers pretty poor opponents in general.
A Beta is less powerful, but 1st Arcturus was fought by an fresh Improved Alpha with 20x X-Rays and 4 Golfs (you may be thinking of Laodemon, which errata'd the Alpha to a Beta).
The TTA issue was solved in the errata. Kafers use UTES. Sinc no Kafer ship has TTA's listed, I wonder what rules you used (although the phrase "The limited number of fire directors on a Kafer ship make it fairly easy to overload its antimissile defenses and land hits, but the sheer amount of punishment a Kafer ship can take can be very demoralizing." is in conflict there).
However, there are a limited number of laser turrets an IA has to oppose incoming missiles, 6, and on average about 1.6 missiles won't make it past the PD and 20% will miss (assuming 2 Kennedy's stacking, say 3 out of 8 are accounted for). The screens value of 9 will effectively take care of a missile, while the remaining 4 put 40 strikes in. 4 hit surface fixtures, 32 are blocked by the armour and 4 penetrate.
Of the penetrating hits, it's probable one will be a critical. The kicker is, the Kafer's CQ is so low she can't repair them. If lucky, and a computer (or maybe drive) critical develops, then the Terrans have won. If their five volleys fail to produce such a critical, they've lost.
If the Kafers fly their fighters in close defence they'll on average knock down to incoming missiles (an average of ca 2 penetrating hits). If they add their own missiles to defensive fire, they'll knock down ca 50-60% of the incoming strike with each wave (of 2 missiles) they commit (and they can probably throw multiple missile strikes at the incoming missile strike, if the Kennedys are holding open the range). A well run Kafer IAlpha (even with a poor crew, that one is -3/0) can prettymuch absorb the missile strikes of a pair of Kennedys and be largely unharmed unless very unlucky.
Try reverse engineering the Bismarck (I think they do it with the Sachsens and Hamburgs as well). The Richelieu should have like 10 pages of hull hits instead of the two provided. The Kafer ships have no technology standard which can be reverse-engineered using the NAM. The weird results I speak of are how armor affects hull hits so you have silliness like single-man fighters with more hull hits than a frigate (the Aconit).
Ahem.
http://www.users.globalnet.co.uk/~dheb/2300/Equipment/SG/Bismarck/Bismarck.htm
(backengineered all three mentioned, only the Hamburg is majorly wrong)
