It is not.
I didn’t write the article. But the feature of canon law in question in the article has nothing to do with presumption of innocence, but rather with prescription (like statute of limitations). Questions regarding presumption of guilt or innocence would be pertinent if canonical trials were being held, but they are not. That is really the exact point — NO canonical process is being used in many cases.
The matter is covered by the commandment, "Thou shall not bear false witness against thy neighbor", which is of course a particular instance of the more general command to "love thy neighbor as thyself".
Anything other than innocent until proven guilty is repugnent to God. So too is the zero tolerance policy, which embraces the concept of "condemnation without just cause" as a particularly good and desirable evil. Where evil is defined as an act which is contrary to the moral code which is the embodied in the commandments.