Well, I agree forcefully, because I use to buy all the fuel I can. But usually, I find at least two stores before ending sector 2. Not only one.
It is for sure some kind of bad luck, but even if you don't check carefully your fuel supply, as Kenshkrix said, it should be possible to exit such dead end beacons.
I like pretty much the "ramming" idea. Why the crew, at the end, annoyed to be unable to shot down such a ridiculous drone, wouldn't decide to crush it against the hull?
Anyway, I restarted my game, only to be shot down in sector 3, with a crystal crew member aboard and the rock homeworlds seemingly insight, because my gunner wasn't able to effectively hit 1 shot by 10... But it's an other story of bad luck.