He must NOT resign at any cost. Let his case go to SJC. If guilty he should be punished. If not, the case should further proceed to see if the intentions of government were malafide. If found guilty then government should be punished as per law.
Petty politics and narrow views from the hatred of the current administration besides, the issue relates to integrity of constitution and the honor of the apex court - and not just some individual judge per se.
In the usual circumstance, he shouldn't resign at this point in time, however if the charges aren't defendable during the SJC proceedings, he should better resign then than to to be punished. That is the tradition of the court for to safeguard the honor of the apex court.
However, the honorable judge has already acted dishonorably by publicizing the case, twice writing unconstitutional letters to president and pleading his case in public. He has already undermined the constitutional authority of SJC badly losing his moral position of the case. So if he resigns now than to further damage the court, perhaps that wouldn't be an unwise decision.
However your comments about the executive are unfortunate and utterly wrong. Not the executive but the honorable judge has intentionally politicized the legal reference using his pets in media and have tried to fight a legal case in public while maligning constitution institutions including presidency.
It is the constitutional duty of the executive to refer a plausible allegation on a sitting judge to SJC, especially when the accused judge has evaded the general investigation by taking shelter of his/her constitutional position. The role of executive is merely as post-office between the alleging body or individual and SJC to fulfill its constitutional duty.
It is very straight forward act but seems unusual only because in the last 70 years we have been addicted to the culture of hiding the crimes of the influential and giving undue favors.
For the sake of nation and constitution, imo you may better had appreciated the executive to hold the influential accountable at a proper constitutional forum. It is so sad that very often the supremacy of law lose to narrow political gimmicks of some misguided individuals. I wont blame you for it as it is an old disease of petty politics.
Your beating over the word 'malafied' is unfortunate as well, since that limits and challenges the scope of constitutional provisions and integrity of SJC. Hope SJC will hold him accountable for misconduct besides the charges in the reference for the sake of our future.