Right now, there's one giant anti-blobbing method being used through the AI Eye, but that's pretty much it for trying to get players to de-blob their forces. Barring an AI Eye, there's nothing encouraging players to act in a more guerrilla warfare style or not use a giant fleet blob.
There are two thoughts I have, small incentives and big incentives.
Small incentives would be something along the lines of destroying counterattack posts when the planet isn't on alert (as in, does not border your planet, has less than 50 of your fleet ships on it or less than 2 of your starships, Devourer Golem is not near) will simply not launch the counterattack. Think of it as the AI not having "primed" their response. Similar for alarm posts, they will have no chance of raising the alarm if their planet is not alerted. It would definitely need a couple other minor benefits to really ingrain this behavior in player's playstyles though.
Big incentives would be the above, combined with an AIP reduction to any damage caused while a planet is not on alert, maybe by 5 AIP or so, not to be less than 1. So destroying a Warp Gate (or alarm post) on an unalerted planet would result in 1 AIP increase (and no chance of alarm), destroying the command center afterwards would be 10 AIP increase instead of 15. Think of it this way: a player loses a command station, they notice because they're given a message saying "blah blah happened!" If they lose a factory, they don't notice unless they're actively building stuff and waiting for things to happen. Same with the AI, possibly - it's "actively" using the command station and warp gates on an on-alert planet (to launch waves and the like), but on an unalerted planet, it may take less notice of what's been lost.