I agree that raid starships are awfully balanced right now because they are HUGELY variable in difficulty between ship caps, game speeds and early game where they are tough vs late game where they are trivial with regards to AI vs Humans, and then turn around and are terrible humans vs AI almost all the time, but there are certainly a lot of things you can do.
Important things checklist:
1) Are you playing on normal or blitz speed with low ship caps (it really should make a ridiculously huge difference in being able to blow up starships, especially with the attack boosts)
2) If it is a big attack and your fleet is brought home to defend, make sure you are being sure to use at least flagships and light starships (munitions boosters if you have them) to break over the armor level better
3) Fortresses will own raid starships, HARD. On normal/blitz, a mk 1 fortress can kill 1.5 mk 1 raid starships every 6 seconds. 3k knowledge
4) Despite what the devs are saying, sniper turrets are still pretty weak on efficiently killing raid starships (9.25 shots to kill mk 1 on normal/blitz), and fighters do relatively nothing since frigates are the UL attack bonus and fighter AP doesn't get anywhere near (Raid Starship armor - Fighter damage per shot). Don't rely on those unless you really like putting 30-40 sniper turrets on two planets and leaving the rest open.
Here is the list of units TO try to use for blowing up raid starships:
-Fortresses (just get fortress mk1. Seriously, do it regardless of raid starships)
-Missile Frigates (boosted with flagships especially) (far less useful on epic speed and/or non-low ship caps because they are already on the damage-armor edge)
-Siege starships (I know radar dampening, but high damage per shot = armor is more trivial. put near CC or WH) (less useful on epic speed, but still ok) (probably don't need above mk 1)
-Autocannon minipods (particularly useful in high cap since they annihilate armor ratings with -1200 or so armor/s at just mk 1 cap, -3600/s with mk1+2 cap) (less useful in lower caps because armor damage doesn't seem to scale)
-Sniper ships (don't know if these ignore dampening, but these are ACTUALLY good against raid starships anyway)
-Spire Gravity Drainers
-Zenith Bombards (see siege starship notes, plus less useful on high cap)
-Just look it up on the reference table for the rest, but the above 4 are probably the best anti-raid SS bonus ships