i think it should factor in at least somewhat, but i do agree that there are more factors at play when talking about best program.
i understand the difference between better "program" and better "team", but take a closer look at what we're actually comparing.
if mj was a 6a program that lost in the 1st or 2nd round every year, i could see more of an argument. but the truth is, mj is competing with the likes of 6a memphis, maryville, and rutherford county for shots at titles, all of whom have excellent programs that are on an at least even level with mt. juliet, while fc was competing against the likes of dresden and adamsville for titles, neither of whom are anywhere near being on an even level with fc.
because of that, i don't think fc's accomplishments the last two years are very much, if any more impressive than mj's two semifinal appearances in that same time frame.