Yes, the principle is - at best - flawed. Even when used in good faith, it is a rhetorical sleight-of-hand, appropriating the very high standard necessary to procure a criminal conviction and demanding that we should not believe a thing to be true unless that standard is met.
"Innocent until proven guilty", in a criminal court, really means "innocent until proven guilty beyond a reasonable doubt". That high standard exists because the State is attempting to judge someone as having committed a crime, and to be subject to deprivation of their liberty and property. The standard of proof in civil courts of law is nowhere near that harsh - even in lawsuits for millions of dollars, the burden of proof is "by a preponderance of the evidence", also expressed as "more likely than not" or "a little more than 50%".
I don't think it's an accident that in discussions like this, especially when the argument is against judging someone's actions, the standard thrown out is "innocent until proven guilty". Doing so evokes a whole set of cultural tropes about the need to protect the accused, the risk of consequences for judgment, and the huge pile of evidence that we demand before we accept something as true when we'd really rather not. Imagine instead saying "I really would want a preponderance of the evidence showing this is true." Just doesn't have the same, all-about-the-principles, Atticus Finch kinda oomph to it, eh?