The problem isn't the AI, because people can and do use the same tactic. "Fixing" the AI so it doesn't use this tactic won't fix the people who use it.
The problem isn't countering this tactic either, since at the bare minimum you can simply ape your opponent and send siege frigs at him too, then see who can bomb who out of existence more effectively.
The problem is different ideas of what should constitute a siege frigate. Picture a typical RTS - Starcraft for instance. You start building your base, everything is coming along fine, when in comes an enemy builder, who starts building a turret right in the middle of your base. You have a turret or two up, which start firing at the builder, but rather than exploding, the builder keeps on building. More alarmed, you select a nearby group of units to come in to fire on the builder, which they do. But as they all concentrate fire on the builder, the builder continues to build. Much to your horror, the builder not only finishes the turret, but then runs off and escapes, while this enemy turret then proceeds to attack your base.
This is the same dynamic that occurs with this siege frigate thing. Builders, it seems, should not be able to get away with the above scenario without dying a quick and painful death. These siege frigs, it seems, should not be able to get away with the above without a quick, painful death. It just sort of flies in the face of what many believe a siege frigate should be, just as that builder does. Nobody would complain if some big, late tech cap ship waltzed in through your defenses and started laying waste to your capital, and even built a turret right next to your planet to bomb it (in fact, one Vasari cap ship CAN build a turret right next to your planet for bombing it).
This problem was actually worse, believe it or not, before the small nerf to the siege frigate. Before, you could have a whole fleet wailing on a siege frig and it would survive for an extreme amount of time. Now, at least they pop at some point, albeit not soon enough.
With a better PJI, this siege frig problem would be less of a problem, because at least they wouldn't be able to make it to your inner worlds without an escorting fleet to take out the PJI. Thus you see how one broken area of the game (PJIs) compounds another area (siege frigs).