Most books have a rule stating that in a situation like yours, the score from before the adjustment is used for grading. Bovada does not seem to have this rule on its homepage:
http://www.bovada.lv/help/general-sports-betting-rules
I looked in general sports, as well as soccer. If this bet were placed at Pinnacle or Cris, which have rules addressing this point, your wager would be a clear loser. You have argument though. As a result of the disqualification, the full match score is changed to 3-0. Their soccer rules are here:
http://www.bovada.lv/help/soccer. One of them states "
4. Unless otherwise specified, the score at the end of regulation play (90 minutes plus injury time) will be used for wagering purposes. Results from extra time, golden goals, or penalty shootouts are not included."
Unless I missed a rule, an overturned result changed the 90-minute result, and the wager should win by Bovada's rules. I'd also note that Bovada's rules -- omitting a clause on disqualifications -- is not the industry standard. By their own rules, matches deemed a forfeit years ago due to NCAA violations would have to be regraded, which is why nearly every book has a rule addressing this issue. But they wrote the rules, and they are an A-rated book. They need to abide by their rules, grade your wager as a winner, and fix their rules going forward.