Not a bad idea regarding the pillar spam, I was also thinking about something similar, but it probably wouldn't be enough still.. spammers would just recruit people to get more flags and dominate places to their likings as before.
I would introduce time and/or "trigger" gates for structure limits, what I mean is, something like: one could not place more that X foundations/pillars on day 1, but as time goes by more and more could be placed (this can be in-game day or real time), this limitation could be reduced by Y if/when a tribe kills an Alpha creature or boss.
This would make bases expand vertically (since there would be no limit on walls and ceilings) instead of horizontally.
An other solution could be to make structures that are not connected to a bigger, multi-structure building decay on a much-much more rapid rate, like pillars with a ladder or a foundation only last like a few hours, but foundations with walls+ceilings/roofs+ramps/stairs etc. would last more (IF they are all connected) the more structures connected the longer they would last (up to a limit).
OR structure decay could depend on what crafting and storage structures are in/on them, the more advanced structures are placed in a building the longer the building lasts.
Dunno, but something must be done with the pillar/foundation spamming situation..
(Agreed on the AFK thing, on launch day there should be a strict limit on how long one can be AFK.)