Was Canónigo Fernández a traitor to Mexico?

There are several things that the canonigo Agustín Fernández de San Vicente may have been in trouble for. Since your source references Pablo Vicente de Solá, we can start with his relationship with the Fernandez. Bancroft records this, in a note in his History of California, pgs 469-470 (emphasis mine):

On the canonigo's character and especially his gambling propensities see correspondence of various padres and officers in Guerra Doc Hist CaL MS v vii passim.
He quarrelled with Santiago Arguello and others about gambling debts at San Diego. P Uria when he heard that the Canonicazo was coming thought it would be a good plan to present him with $2,000 and a dozen packs of cards. Sola accused him of intriguing to keep him out of congress, of committing scandalous acts both in California and Mexico, of leaving unpaid debts at the capital and of abandoning in Mexico one of the Russians he had brought with him and from whom he had borrowed $497. Malarin had something to say about his debts and fondness for display. Vallejo, Hist. Cal. MS i 323-7, says Magin was so horrified that he requested Fernandez to quit Sta Clara. He also alludes to the races and bull fights given in Monterey in honor of the comisionado. JJ Vallejo Reminiscencias MS 79-81 speaks of his immoralities as does also Alvarado Hist CaL MS i 216-17. August 2, 1823, Ruiz to Guerra mentions report that Fernandez is a prisoner. Guerra, Doc Hist CaL MS v 221 Appointed vicario of New Mexico. Mexico Mem Justicia 1826 18-19

That Sola 'accused him' sounds a little more formal than just a complaint. Another possible area of contention can be connected to Bancrofts' above passage, one of the correspondents of the August 2, 1823 letter mentioning Fernandezes' imprisonment. Guerra.

This would be José de la Guerra, referenced here, (Bancroft, pg 465):

Chosen as deputy and engaged in preparations for departure Sola had notified José de la Guerra to be at Monterey by the middle of July to assume the command As the senior ofiicer in California Guerra was entitled in the natural order of things under the old system to become acting governor until the regularappointment of a successor to Sola and no other officer was thought of for the position

...on October 1st Sola announced his intention of sailing in the San Carlos and summoned Guerra to the capital. The captain was congratulated by his friends who expressed the hope that the appointment would be made permanent

It was a 'natural' step for Guerra to replace Sola. But the canonigo apparently had different thoughts on the matter.

When the canonigo heard who was to be intrusted with the temporary rule he suddenly discovered that his instructions required the acting governor to be chosen by a vote of oflicers He knew the growing feeling of bitterness against the Gachupines or Spaniards in Mexico and he did not deem it conducive to his own personal influence and popularity to return to Mexico with a report that he had left a Spaniard in command of California

So Fernandez upset the 'natural' order of things, to manipulate the situation in a way 'conductive to his own personal influence and popularity'. The 'voting' process involved appears to have been suspicious at best, and of course resulted in Arguello being Governor, and not Guerra:

So of course it was decided The diputados voted solid against Guerra, and Captain Luis Arguello was elected by a majority of one or two probably on the 9th or 10th of November. Don José was bitterly disappointed and his friends were indignant Arguello was not blamed at least not by Guerra who had always been and continued to be his warm personal friend but charges of corruption were freely made and the vote of the diputacion was said to have been bought Some dwellers in the south were inclined to take a sectional view of the matter and regard the election of Arguello as a dangerous triumph of the north.

So, quite a few individual were not happy with this action which Fernandez had taken. Individuals in the South (Mexico), who probably maintained some power after Iturbides' fall. A couple more clues can be gleaned from one of Bancrofts' notes again:

Jan 2 1823 Narvaez advises Guerra to abide by his fate but yet lay a complaint before the supreme government of the gross slight inflicted on him.

Feb 10 1823 Manuel Varela from Tepic that the canonigo expressed regret at not having left Guerra in charge but that he had acted on the advice of the padres who thought i the present condition of the troops it was not best to keep the hawser to taut. Guerra Doc Hist CaL MS vi 135

So we can see it was recommended in Jan. for Guerra to file a complaint, and by Feb 10, 1823 Canonigo Fernandez was answering concerns as to why he had not placed the stronger Guerra in charge. The timing of all this information seems more than coincidental. Feb 10 'expressed regret", charged with treason July, letter to Guerra telling of imprisonment on Aug 2.

Bottom line, Fernandez had several things to answer for. His association with Iturbide may have protected him for a time, but when he lost that protection he had to face the powerful friends of those he had irritated; Solas' accusations and Guerras' friends. Without actual legal records from the time, we may never know the actual charges made. Since he survived to be placed as vicar in New Mexico, we can assume he was deemed not dangerous to the new nation, and that his intent wasn't treasonous, just immoral and misguided by self-interest.

(If I missed any citations, all the above quotes are from Bancrofts' History of California, and all emphasis is mine. Apologies for any OCR errors I missed.)