Two minutes wouldn't be enough though. A significant portion of the warzones I play we start out with 5-7 players; essentially all of them would become non-starters (not full at the two minute mark) and I'd end up joining the game, loading, waiting, get kicked, load planet, and re-queue. Seems worse than the current situation to me since those games almost inevitably fill up within a few minutes after getting started and few and far between are the games where anything is actually 'decided' that quickly, at least due to player count disparity that is.
Voidstar is the worst case scenario as if the attacking team gets 'behind' (ahead?) of the defenders you can essentially get blitzkrieg'd; but again, that's the worst case scenario and due more often to unlucky respawn door timers above all else.
Civil War it's minor, by your logic whoever gets two points first wins. What determines Civil War though is organization and communication more than anything else; I've won my fair share of comebacks and lost to a lot of them as well. Even with a bad start, you have plenty of time to recover. If you can't take a point it's because your team can't take the point, not because the other guys got there first, especially since the side-speeder timer was put in place.
Quick scores in succession in Huttball are almost always the result of a premade on the other team, completely different cause. In which case, you're kind of screwed regardless of how many people are on your team. Huttball as a premade against a group of PUGs is almost impossible to lose if you communicate with each other just a bit.
Random players against random players, it's hard to see them really scoring more than once (at most twice) before the other team fills. In which case that's really not that difficult to overcome considering the time given to you. Not to mention most teams have the tools to easily prevent scores even with fewer people; but I think what's more important is whether people are cognizant enough to use those tools effectively instead of how many people you can throw at the ball carrier.
And what I'm saying is that you get a free win as often as you get a fast loss. It affects everyone equally and evenly and not that commonly nor that greatly. On the list of what determines who wins a warzone, starting the match missing a player or two is close to the bottom next to "faction imbalance" and "datacrons".