I don't think the NFL should give them back. There was an appeals process. The team specifically waived their appeal rights. Now, for better or for worse, they're stuck with the judgment.
I certainly don't believe the league will give back the picks.
I think they "should," if they were at all interested in giving out fair punishments for crimes committed. However, it is abundantly clear this is not and never has been Goodell's goal.
Your comment is an interesting philosophical question. Hypothetically, for example, if we were talking about criminal guilt, should only people who initially appealed and lost their guilty verdict be released from prison if exonerating evidence was found after the fact? If the state found overwhelming evidence of not-guilty, I would hope that they wouldn't say "well, he should have appealed in the first place" and just discard the evidence.
That's not how criminal law really works. If there's exonerating evidence that wasn't discovered at the time, a defendant will get a new trial.
In civil law, it happens all the time. If you lose, and don't appeal, it doesn't really matter what happens after the fact. Generally speaking, a judgment is a judgment.
I realize that criminal law would work differently, but philosophically, the principal should be the same, if the goal was actually integrity, fairness, and/or justice. The league isn't even a justice system, so they are not bound by criminal nor civil laws in terms of internal regulations (Their practices must still adhere to applicable external law, which, so far, in the case of Brady v NFL, they have not as determined by Judge Berman).
Point is, the decision to appeal (or not to) is often independent of status of guilt. Therefore, if guilt later becomes significantly doubted, the punishment "should" be altered, regardless of appeal status.