Out of dozens of sova rushes either made by me or made on me, the only defense I can see that works are the presence of some sort of long-range attack craft, if TEC then lrms, Vasari then assailants, and so on. The problem is, with Advent, because of the much higher cost to get to that stage, and because a sova rush can occur before you even get your first asteroid, as far as I can tell, unless you have some really good teamates who can quickly counterattack the person rushing, then there is no defense. The problem is most teamates I've seen on the boards are too stupid to understand the importance of such an early shut down in an economy.
Any direct assault with a cap ship vs the sova will fail if the person making the rush has half a brain since the sova can cruise continuously just out of firing range, using its bombers to slowly kill your own cap ship. Your disciples or cobalts can peck away at the shields of the sova, but at the time of any sova rush it is unlikely you will have many frigates, and of course won't be able to make many after the rush. Besides, the sova usually kills the frigate factory first if it can, although because of embargo, it really doesn't need to. I have tried the direct assault approach several times and it always ends up with the sova killing my cap ship (no matter what kind) and my starting frigates long before my ships can kill it.
After finding a direct assault could not work, then I tried continuing to colonize to (1) improve cash and resource flow, (2) possibly get to the long-range assault craft stage which could then stop the sova. If you are TEC or Vasari, getting to the long-range assault craft stage is not too bad, and is occasionally doable, but with Advent, basically impossible since by the time you start getting illuminators out, enemy teamates are already probably converging on your stricken homeworld to assist the sova rush.
The other option, which I suspect will still disproportionately cripple you anyway, is to take some newly colonized planet and switch your homeworld status to it, thereby removing the embargo from your most important economic world. Of course, switching homeworld status so early in the game is a bigger economic catastrophe than losing your first cap ship. Also, if the person behind the sova notices the switch he can also simply jump to that planet and start all over.
As far as I can tell there is no strategy to defend vs. an ordinary Sova rush for Advent and that is a serious oversight. The issue is mainly timing since even if you are alerted early enough to it, even if your first scout goes straight to his homeworld and sees it coming, there is not enough time to prepare if you are Advent.