Here are some other approaches I haven't seen yet, that might help get past the "unstoppable in a blob" vs "obsolete" dilemma.

1) Planet bombing as an anti-matter ability.

As anti-matter is drained by phase jumps, this would nerf the jump-bomb-jump-bomb raids. Siege frigates could still do some serious damage, but they'd need time to get started, and would be less able to fly deep into enemy territory and destroy a planet before the defender could react.
In addition, anti-matter stealing/skill disabling can now be used to delay sieges.

2) A "set-up" time before firing/bombing

Not unlike the Assailants "disable your drive to fire more" ability, this would disable the siege frigate's drive once it is in position, diverting all power to the main weapon. At the moment the skill is activated, the drive is disabled for say 10 seconds and at 10th second the weapon fires. Obviously, one shot would do more damage to maintain the current dps, but it would make the frigates much more vulnerable to counter-attacks.

3) Flying bombs

Sins' siege ships are loaded to the brim with huge guns, volatile explosives and/or oversized nuclear reactors. What would happen if the hull got penetrated by a glowing ball of plasma or phase missile? I'd say AoE on death >

4) Slllllooooooowwwww

You need huge weapons to damage a planet, but you don't want to spend the credits to build a capital ship? Just stick on a basic frigate drive and you have a flying gun. But wait, you also need ammo stores, armor, controls, fuel...
You get the picture, this thing will always be last to the party, just in time to mop up. And that's exactly what they're for.
Make siege ships powerful, but slow enough to be a hassle. Can't keep them with the main fleet, can't easily escape. You could combine this with #1 and give them a "faster, but drains antimatter" skill to at least get them near the frontlines before the game is over.