1) Using unnamed sources to discredit another previously unnamed source does nothing to establish your credibility. The way to redemption in a case like this is to lay out all the facts and figures. If you are withholding facts pending a criminal investigation, you should say so, and later disclose those details when such investigations are complete, and in a timely manner.
2) Many of the details you omit would not be prejudicial to a criminal investigation and should be disclosed publicly without delay. Particularly many more of the details regarding this "Mr. Wilkinson", whom you freely name, and specifically how you came to verify and trust him as a source. The key word to your story, in more ways than one, is corroboration, and that requires details that we and your colleagues can check for accuracy. Withholding such details would be suspicious to the point of self-condemnation.
3) Deleting those stories of yours that you claim are tainted, rather than revealing what elements they contained that you are now disavowing, is not a retraction. Having made the admission you have made, it is incumbent upon you to publicly address the validity of each and every story you have written that may have been compromised by this corrupt source. That is by means a simple or painless task, but attempting to hide these stories instead is tantamount to an ersatz coverup, and is questionable in motive.
4) In brief, if you are choosing to come clean, then there is no benefit to only coming half-clean, anymmore than there is benefit to washing only one half of a dinner plate. The veil must be lifted entirely for the truth to be revealed. You have talked the talk, now it is time to walk the walk.
An apology made in earnest is a brave and commendable act. But an apology made in dishonesty or deceit is beneath contempt.
It is now up to you to establish for your readers which type of apology this is.
We'll be watching.
Imal