Agreed. For better or worse, Marrone left before the job was finished. There is no doubt that he made the team better, and took a program that was the dregs of the P5 and made them more competitive in year 1. The 2011 ups and downs are forgivable due to injuries, and we pissed away a Rutgers game that would have qualified us for three bowls in a row.
I don't think that anybody can begrudge him for leaving to take an NFL job. But as I recall, a lot of the hand wringing wasn't about his decision, but rather that the team was at a critical juncture after the 2012 season and was losing a lot of talent [in truth, the majority of the key offensive principals responsible for the prolific success experienced in 2012]. Adding to that uncertainty was the decimation of the staff.
Again, nobody begrudged him taking one of the 32 top jobs in his profession, the money associated with that, the prestige, etc. It was more about the condition that he left the team in, the staff being depleted, him leaving before the rebuild was "finished" and the results more sustainable, etc. Marrone left on a high note, but one where the team was teetering on the precipice, and could easily backslide. Guess what happened?