Innocent until proven guilty is a nice idealist concept, but if you have ever been falsely accused of a crime you soon find out it doesn't exist.
To me it's the FA that comes off looking badly here, they should have continued their investigation, made their decision and if warranted, dealt out any punishment. There has been cases in other sports where the authorities have carried out internal investigations ahead of criminal trails and they have not seemed to prejudice the upcoming trail.
The problem the FA faced in this incident, is that anyone in the public eye whether in the private sector or the public sector who faced similar charges would have been suspended while the investigation was on going. It seems that the FA was hoping the courts would deal with this before the end of the season and they would be off the hook in regards to having to make a tough decision.
The FA's inconsistency in similar cases has come back to haunt them here. Woodgate and Boyer where suspended from England duty once they were charged with the assault of a Asian student, and Rio Ferdinand was suspended from England duty once he was charged with missing a drug charge. However Gerrard was allowed to play for England while he was on trail for assault.
No matter what the FA decided on this case, it was going to look like a mistake, they have mishandled it from the start and left themselves little options.