AFAIK, we haven't been in this position for any real qualifying matches, but I can see what you are saying.
Yes, it does suck not having a full alliance. Yes, it does put you at a significant disadvantage. But this truly is part of the game.
Really, their 'bot not working is not just their fault. As an alliance, (at the risk of sounding insensitive) it is partially your team's fault, too. Well ahead of time, you should ask the team how they are doing. Check if everything is working; check if they need help. We have done that more than once--we helped a team at West Michigan; they wouldn't have been able to pass inspection if we hadn't helped them out. This is something the competition is designed to encourage.
And there is an element of luck. There's not much you can do about that.
I'm not trying to be insensitive. Please don't take this wrong. But I don't think there's anything FIRST can do to level the playing field here. Not to mention it would make the match generator's job even more horrible...
JBot