The Jefferson Davis Papers project at Rice University has a brief discussion of "The Case Against Jefferson Davis" on their website (see link below). According to them, Chase's opinion is based on the 14th Amendment nullifying the indictment, not his belief in the legality of secession. I would be interested to read the law review and journal articles cited at the end of the article. If anything, Chase's concern about an acquittal seems based on the difficulty in securing a conviction with a Virginia jury based on popular rather than legal considerations.