"He faced up to 90 years in prison." I think that, all things considered, this is the best possible outcome (realistically). There was no way he'd walk, because he did break laws. In this instance those laws were broken to get information out to the public, but one can easily imagine when those laws could be broken for more malicious purposes. If you leave this unpunished, they might think this opens up the floodgate…
I'm not going to comment about the length of the sentence itself. But sentencing is supposed to take into account the exact details of the offence. "one can easily imagine when those laws could be broken for more malicious purposes" is a reason why somebody breaking laws for more malicious purposes should get a longer sentence. So your argument actually works the other way: it explains why Manning might have been expected to get a lesser sentence.