No, not nessesaly.
To aid and abet/permit /allow you have to do something active to assist or allow it. This is now departing from your senario.
Dealing with the subject of this first. You say the ATCO is innocent. If thats the case then you can't aid and abet an offence if hes not committed one.
I suspect that in this case they have cocked up, should have called the police and didn't. Sought advice, then found out they had cocked up and are now going down a discipline route. Yes in terms of reasonablity the fact that the ATCO was allowed to continue working gives him a huge defence (if he was allowed to continue to work) afterall if he was causing a problem or dangerous or they thought he was committing an offence he should have been taken off controlling duties, if he wasn't then he can't have done anything wrong.
In general, well thats a whole differant can of worms. knowing or believing someone has committed an offence isn't assisting them. If you saw a person nick a bar of chocolate and did nothing about it, would you say you were guilty of aiding and abetting theft? No, you wouldn't. If you saw someone get in thier car that you had just been with when they drunk 10 pints, would you be guilty of aiding and abetting/permitting/allowing him to drive while drunk/over prescribed limit? No.
The full facts would have to be investigated and then a decision made. Some offences purly having knowladge of the offence or intention makes you guilty of the principle offence. In others it does not. The intentions and knowladge have to be looked into before you can allege that someone aided, abetted, assisted or permitted an offence.