The "Find and delete malicious emails" page in the Google Workspace Admin Help Center states:
Using the investigation tool, you can identify all users in your domain that have received the message (for example, a phishing email). You can then use the investigation tool to delete the email from your users' Gmail inboxes (note that log data might take up to a few minutes before being available in the investigation tool).
From this, I understand that, assuming you have the right package, it is possible to use the investigation tool to delete the unwanted email from your users' Gmail inboxes.
Can I delete emails from my users' Gmail inboxes via Google App Script using the API? If so, how can I do that?
But there is already an existing feature request for exposing the Google Workspace Investigation Tool programmatically.
I recommend you to "star" it to show Google that more people are interested in this feature - hopefully this will accelerate the implementation.
UPDATE:
In th meantime you can use a workaround, e.g. using a service account with domain-wide delegation as suggested by @TheAddonDepot