I can't say that I think they're trying to nerf "throwaway" planets (even though they're far from that), they're just trying to make things more consistent. The AI doesn't currently have the logic input to take time to fully clear a planet. This is good because it keeps the pressure on a player by not allowing the player to stall out an AI offensive by having too many targets for the AI to clear. So an assumption is made that the AI wouldn't normally leave planetary infrastructure intact, so the self destruct mechanic is implemented as a gameplay streamlining thing - the player gets plenty of those, so it's not all that problematic if the AI gets a few.
That being said, there is no such thing as a throwaway planet if you're playing at a difficulty matching your skill level because of the AIP cost as soon as the command station goes boom, so really there's nothing to nerf.
If you're having a problem with needing to constantly rebuild your planets, there are steps that can be taken to mitigate that. Unlock more turrets, fortresses, and forcefields, or use more (and higher tier) logistics stations so that your fleet has both the speed and the time (by slowing AI down) to get where it needs to be. Learn AI attack patterns, because often you'll hit a point in the game where most CPAs, carriers, and exogalactic strike forces will follow certain paths, and you can generally control where waves go. Make use of the Alert mechanic on your border planets so you don't get caught unawares, and disperse your mk1 scouts along those border planets so you can monitor fleet buildups. Having a fleet of transports available can also help, since they're generally faster than most of your ships. Load your fleet into the transports when an attack happens, and zoom them all off - they'll deploy instantly on friendly planets, so it's all good (and no waiting for the missile frigates). If you've unlocked the mk2, your fleet will always be in top shape without having to deal with engineer interference.