Personally, I'd like to think one of two things happens.
1) Eli fixes it but loses his frakking mind in the process
2) Eli fixes it and goes into stasis and season 3 begins with Destiny dropping out for a dial-in from Earth with Telford knocking on the glass of Young's pod like "Wake up sleepy head!"
What would be particularly awesome is if they did something where it takes WAY more than 3 years, Destiny recharges, never wakes them up, and Earth dials in with some sort of way to retrofit Destiny with ZPMs that we can now create and the crew has the most badass ship on that side of the universe.
Ahh... a guy can dream
/side note: do any of you guys subscribe to MGM or Syfy on Facebook? Neither of them---especially MGM---can even post anything to this day without getting bombarded with requests for more SGU. It's absolutely amazing to me because it never actually seems to be the same people...