First: because it's really hard to pinpoint exactly who is responsible for something like this in a large organisation. Is it the CEO? They are unlikely to know enough about French taxation. Is it the local accountant? That's probably a team as well.

Second: Cases like this often arise from different interpretation of laws that are all at least plausible. Companies may tend to be somewhat too optimistic in their interpretations, but it's rare, at least at that size, that they actively try to commit tax fraud.

Third: It is the company that profits from the offense, so it's only fitting to apply any sanctions to it.

Fourth: Making this criminal law would raise the required standards of evidence to a level where few of these cases could ever be prosecuted.