iMaple
I wouldn't normally make this sort of massive game-changing suggestion, but you made it very clear the game is in early alpha, so here goes:
Take a page out of Grand Strategy/Stellaris in the option of vassalizing conquered players instead of outright removing them from the game. I have currently no idea as to how the game plays out just yet (I will give it a try later today) but you mentioned a lot of small-scale conflicts early on. Imagine if at the beginning of the game a player is ganged up on and quickly eliminated, especially one who spent money on the game (as much of a taboo as this may sound). They were just thrashed, so they don't get to play for the next several months and may just give up entirely on the game as a result.
If you offer player vassalization instead, after being conquered the player remains in the game, even if subordinate to someone else. Although slim, there is still a chance for them to grow and participate and possibly even overthrow the ones that conquered them. I think that is the big difference between a multiplayer game of Stellaris and Endless Space; it is not a deterrent in ES as the games are relatively short, but for something massive like Starborne where a campaign will last months and months it might be the deciding factor over whether a player may quit or remain.