Are you using your entire blob for that kind of stuff Red Spot? Because that's not so much a guerrilla raid as a full-on frontal assault. The whole game does not beg guerrilla raids; outside of AI eyes, there is nothing in the game that provides an incentive to use 50 ships instead of your entire fleet.
This is not about neutering planets either. This is mainly about surgical strikes on key AI installations to deal with particularly problematic AI defenses that happen to be underdefended (counterattack posts, alarm posts, raid engines, etc. that aren't under forcefields, or are on poorly defended planets). If you send your full fleet in (as you currently do), that stuff is going to trigger, guaranteed. If you send in a small strike force, you can get around that trigger but it's not always going to be possible, and you can't have a giant fleet on the planet next door either.
This is very much not the way you just described how you play the game; you say you wipe a planet clean, then wipe the next planet clean before you take the first planet. Doing that (under the Strong version of this incentive) will cause you to take full AIP penalties at both planets. If you sent a small strike force to the second planet before you take the first planet (and you haven't alerted the second planet through any of the given means), then you can take the planet for about half the normal AIP at the cost of not having it be neutered already, and not having the planet between you and your new planet be neutered until you send your fleet to clear that one. If you're willing to attempt the small deep strike force, you can take 2 planets for 31 AIP instead of 40 AIP, but you'll have to deal with the counterattack when all the guards go on alert and attack.
Edit: I've made this change to the proposal, as a counter to potential abuse.
For the "strong version," destroying an AIP increasing target on an unalerted planet will decrease the AIP gained by 5, to a minimum of 5. That way it applies to larger things like Command Stations, the occasional Raid Engine, Black Hole Machines and Grav Drills, but it won't let players willy-nilly run around and destroy all the warp gates in the galaxy for 1 AIP each.