I don't think Mike Smith told his OL to hold on the first running play, thus stopping the clock. I also doubt that he was calling the plays. All they needed was to do was kneel down 3 plays and they likely win.
Now, having said this, the problem with the Falcons starts with Arthur Blank. He is the one who hired and kept Rich Mckay, and he's the one who went out and hired Thomas Dimitroff. He was also the one who was in favor of the Julio Jones trade where the Falcons net lost 4 draft picks. He is the one who has pushed the marketing "offensive agenda" of the team at the expense of the defense.
Mike Smith's history is as ma defensive coach, so don't think for one minute he is the one who has been happy watching the falcons allowing their best players to leave, and end up being a team with one of the lowest defensive payrolls in the NFL. when your own brother-in-law says you have the worst defensive talent in the league, that says something. His BIL is Brian Bilick.
The bottom line is simple, even without injuries, the Falcons have little talent on the defensive side and the OL has generally been sub-par, of course they let several high quality guys go via FA a few years ago.
Smith will be gone at the end of the year, but he is not the major problem with the Falcons.