Less than 12 hours on from O'Brien labelling the draw as "ridiculous" after Kalyn Ponga sat out the 20-6 loss to St George Illawarra, the Knights suffered another blow on Saturday.
Thompson was hit with a grade-two charge for a crusher tackle on Hamish Stewart, with two previous offences since late last year meaning he is facing an extended ban.
The Kiwi front-rower can accept a four-match suspension, or risk a fifth on the sidelines if he fights the charge and loses.
Thompson's ban will do little to ease pressure on O'Brien, with Newcastle having won two of their last 10 games and on a downward spiral.
Ponga was part of the Queensland side who lost the State of Origin series opener on Wednesday, but at O'Brien's insistence was put on ice for Friday's loss to the Dragons.
The fullback has been carrying an ankle injury through the Maroons camp but is expected to play next Thursday's home game against Manly.
O'Brien said he rested Ponga for his own good but claimed his side had been given no favours by the NRL's draw.
"In this battle we lost to the scheduling and the draw," O'Brien said.
"Someone has got to play Friday … we get that but then they hit us next Thursday as well so it would have been three games in eight days (for Ponga).
"I always knew that once the draw came out we would cop the Friday after Origin, but it would have been good if someone said, give them the Saturday or the Sunday the following week.
"But whoever does the draws either hasn't lived it or doesn't care, so I don't know which one it is.
"You have got teams like Canberra who haven't had a bye yet and then you have got teams who haven't left home in seven games in a row. It's ridiculous."
Newcastle's loss followed an encouraging win over a Penrith side missing five players to NSW Origin duties a week earlier in Bathurst.
O'Brien's men remain within touching distance of the top eight but they will need to go up a gear over the next month, where three of their four games are at home, if they are to make the finals.
The Knights are hopeful of having Greg Marzhew back to face the Sea Eagles next week but Bradman Best and Jacob Saifiti remain a long way from fitness.
"I think within the next month, we should get the majority of our personnel back on deck," O'Brien said.
"You're always concerned a little bit, but you can't get caught up in (who is available).
"We've got to get caught up in playing Manly at home next week and making sure that we get that right and fixing some of our discipline."
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