No this is the problem, it doesn't work. There isn't enough teams searching. AT team queue would be 30 minutes. It was nearly impossible to get a AT 3v3 or 4v4 game in CoH1 because of this. And by taking away the possibility to get a match in a timely manner as arranged team, you would kill a large portion of the community.
And if it was an option, then every random would disable it obviously LOL.
I think a better solution would be to (almost) remove any ELO penalty that you get as a random if you lose vs a premade team.
Why wouldn't you simply play 2vs2 if you are 4 friends? Do you think it is more interesting/accomplishing to wreck randoms than having a fair game between your friends?
Coh3 is probably going to have the same hard learning curve than its two predecessors, no need to add a other layer of exasperation with AT teams vs randoms.
Your proposal isn't going to be any better than disabling AT vs Random since as random you'll just quit asap with no penalty once you know your opponents are a team.
Edit: thinking about it, IMO, best solution would be a mix:
1- Random can disable auto-match vs AT
2- Random get ELO decrease reduction when losing vs a team
3- Random get ELO majoration boost when winning vs a team
So you make sure randoms that are willing to play vs team do it with a reason. Only CONS is the possible abuse some players could do with it.