Why was Will Graham not charged with the attempted murder of Hannibal?

Will Graham would probably be an accessory to or an accomplice to murder, since Will Graham didn't physically do anything, being behind bars at the mental institution. These alleged charges might have dropped with all of others, when they were able prove that Hannibal was the Chesapeake Ripper & the (Hobbs) Copycat killer and that Will Graham was innocent...

However, it should be noted that one of the later novels, specifically the self-titled Hannibal novel (and film adaption) change the vantage point of the previous books (Red Dragon, Silence of the Lambs) by making the FBI appear to look corrupt, as the character Paul Krendler, is Clarice Starling's nemesis within the Bureau and Clarice is abandoned by father figure Jack Crawford, grieving for his the loss of his wife. (This all serves Clarice's transformation at the end of the novel).

Hannibal is a novel by American author Thomas Harris, published in 1999. It is the third in his series featuring Dr. Hannibal Lecter and the second to feature FBI Special Agent Clarice Starling. The novel takes place seven years after the events of The Silence of the Lambs and deals with the intended revenge of one of Lecter's victims. It was adapted as a film of the same name in 2001, directed by Ridley Scott. Elements of the novel were incorporated into the second season of the NBC television series Hannibal, while the show's third season adapted the plot of the novel.

The TV series may have been trying to incorporate those elements much earlier than the source material reveals them with both the absence of prosecution for Will Graham's attempted murder on Hannibal, but more so in looking closer at Jack Crawford's ethics, where he was warned by Alaina Bloom not to push Will Graham, believing that he would get too close and he would break.

Kade Prurnell is a pastiche of Paul Krendler, Clarice’s bureaucratic and misogynistic nemesis from The Silence of the Lambs and Hannibal. The original plan was for the character to be gender-flipped as Paula Krendler, similar to Alana Bloom and Freddie Lounds, but MGM holds the rights to the Krendler character since he first appeared in The Silence of the Lambs. Prurnell’s name is an anagram of “Paul Krendler.” According to Fuller, the use an anagram is in itself a playful reference to Hannibal's fondness for anagrams in the film adaptation of The Silence of the Lambs ("Miss Hester Mofet" and "Louis Friend" for "Miss the Rest of Me" and "Iron Sulfide," respectively).

They also created (due to copyright issues) a character whose name is an anagram to Paul Krendler's named Kade Purnell. She begins to be either a nemesis, monkey wrench, or devil's advocate to Jack Crawford, but ultimately showing a political hierarchy from within the FBI.

All in all the absence of prosecution, despite it being part of a deal or not, could be a symptom pointing us to this theme/concept.