Shivan primaries are nerfed to give the player a fighting chance. If they were made stronger, all of Alpha 1's wingmen will die in two minutes.
Also keep in mind that the Kayser is derived from Shivan weaponry, so Shivan lasers should theoretically have about the same damage rates as the Kayser.
Not necesarily.
In COTS I've set all enemy weapons to be 2-3 times are powerwfull compared to stock (damage and rate of fire). It's true that you can no longer chase after a target while being shot in the rear - oh no, you better EVADE those shots mister!
However, it might be prudent to give the players wingmen a higher AI setting. There is a difference in how long they survive, but it's a very small one.
Note than I'm testing my missions with those weapons AND a custom AI profile where the difference between difficulty levels has been greatly reduced, so the AI isn't so gimped on lower settings. Normal is the new hard (to put it mildly).
And I still can get trough missions without loosing almost any wingmen.