"... oder all eure Mühe war vergebens." is entirely OK in day-to-day colloquial speech. People tend to be sloppy in direct speech, and they would get across what's meant.
A 100% properly formed sentence would actually ask for subjunctive, and a complicated one (future tense II to indicate an irrealis of the future, and thus Konjunktiv 2 - It's probably not going to happen). The fact that the effort was wasted would only occur in the future, and it must be irreal. So in order to keep things happening in proper grammatical order and mode, you would have to say:
Ihr müsstet das erledigen, oder alle eure Mühe würde vergebens gewesen sein.
But absolutely nobody talks like that and it's entirely over-complicated. People tend to work around the subjunctive, and also around any possible forms of future tense in day-to-day speech.
Ihr müsst das erledigen, oder alle eure Mühe war vergebens.
is thus absolutely fine.