Ouch, border aggression can be nasty, especially when it is higher mark planets doing the border aggression freeing.
The key is to make sure that you have enough of a force to deal with it by the time it starts, and try not to keep high mark planets alerted too long.
But if you do trigger it, sadly I am afraid I can't offer you much advice, as I don't usually face large amounts of border aggression before I have much to my name.
And yes, I would agree that spire railclusters are somewhat OP right now. At least a cap of standard fighters should have about 50% chance of winning an equivlanent mark cap of sprie railclusters.
However, as noted, your situation is somewhat skewed as you are facing Mk. IIIs relatively early in the game.
Though that brings up one very good question, why are you facing border aggression at only a few hours into the game? It usually take much longer than that for things to build up enough (not just alerted planets, but other non-alerted planets the AI is allow to "overflow" into when the alerted planets get near full) for border aggression to start happening, even if you leave a single planet alerted for that entire time since game start.
(Note, I am not blaming you, I am saying something seems odd in the AI logic in this case)
EDIT:
I dunno - are there not other tools' in the payers arsenal (starships, mainly) that can deal with railclusters?
Probably. I don't mean so overpowered that they can't be dealt with at all (there's always warheads, after all), just that the numbers are suspect since (iirc) they still have the original numbers I assigned them from the dps guidelines when I created them. The case in this thread is the worst I've heard about them, but it's not the only feedback I've received that they're OP (in both human and AI hands).
IMO, they are not hideously OP, or even crazy OP, but they are OP enough such that if you face a wave of them or try to tackle a planet with reinforcement preferences with railclusters as one of them, it can be rather aggravating.