Well, I know a reblance of average "normal" ship stats and average superweapon stats is on the table, but until then, what about ways to help make superweapons a little less squishy in the short term?
One of the notable offenders of superweapon "squishyness" is the anti-starship guard post. I was thinking, if most of the superweapons have ultra-heavy hull type, but most of the starships have heavy hull type, what about giving the anti-starship guard post a .5 or .25 damage vs ultra heavy? While your at it, maybe 4x or whatever the attack strength of the OMD (at least enough to tie with the mk. III anti-starship guard post, maybe even mk. IV), but give it the same penalty?
This is a temporary measure. Once the rebalance of superweapons happens, this change SHOULD be reverted, reapplying it only if reverting it hurts balance too much even after the rebalance.