If he was arrested in 2000 then pretty unlikely that his employer did not know............getting arrested and charged with impact on life when it is going on is not something that can be hidden easily.
Given nature of what he was arrested for and close ties that have always been between BA and Met Police it is inconcievable that BA were unaware of his arrest even through unofficial channels.
Sadly this is likely to end with a load of white paint and an undisclosed settlement.
Question then is are there any more individuals doing this and what will BA now do regarding its staff during layovers.