The 20-year old pleaded guilty 'to lewd, libidinous and indecent behaviour towards two under-age girls' but has been kept on by club owner Vladimir Romanov.
The decision has outraged the Edinburgh club's supporters as well as Jefferies who had no hand in making the decision to hand the player a reprieve.
But Jefferies says his hand may be forced to keep Thomson sidelined because of the severity of his actions.
"I knew what the reaction would be and he can't have any complaints because it was a bad, bad thing he did," he told the Daily Record.
"One of the worst things it's possible to do. He has made a grave error.
"It gives us a situation. We have to make sure if he ever gets back in the team - and let's not forget there's competition for places - how would he handle what's coming to him.
"We have to be sure because at the end of the day that's going to affect the performance of the rest of the players.
"We can't allow it to become a bit of a sideshow which gets out of hand.
"I think he would be going into something he has never been prepared for. He might find it will be tough for him from now on.
"But the board have made their decision regarding the matter. It's not an ideal situation."