Hamilton, whose lead over Ferrari's Sebastian Vettel in the standings is now 50 points heading into the Japanese Grand Prix this weekend, said he was "the most conflicted I have ever been" after taking the chequered flag in Sochi in such a manner.
Hamilton will head into the concluding five rounds of the season with a 50-point lead over Ferrari driver Sebastian Vettel following his win at the Sochi Autodrom.
"I don't think it is fair now asking them tough questions".
Wolff will also be tasked with ensuring Bottas' confidence is not dented as Mercedes go about closing out the constructors' title.
Bottas said the decision was "confusing" and that he was not prepared for it.
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"It's actually quite a hard day".
"So how are we going to finish the race?"
"I don't know, we're a bit behind in pure speed, but in the race the auto feels OK".
The Finn and 2007 world champion is keeping his F1 career alive at Sauber for the next two years, but Hamilton thinks Ferrari is making a mistake in letting him go.
After a slow pit stop, Hamilton briefly found himself behind Vettel before completing an audacious overtaking move on the German to reclaim his track position.
The decisive intervention came on lap 23 of 53 in the race.
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Bottas, who signed a one-year extension in July to stay with Mercedes next season, added: 'I am prepared to play for the team.
Sacrificing the win meant Bottas is still waiting for his first victory of the season but he said it was easier to do now as "there is nothing I can really achieve that really matters to me", even though he has moved ahead of Ferrari's Kimi Raikkonen into third in the championship.
Bottas, who started Sunday's race 110 points behind Hamilton and out of championship contention, had pleaded to switch positions back with his team-mate shortly before the chequered flag, but his request was denied.
A famous victim of team orders, Felipe Massa has nonetheless backed Mercedes' decision to rob Valtteri Bottas of victory in Russian Federation.
Wolff said: "Rationally it was the right call, but our sporting heart says no".
With damaged tyres, they were anxious Hamilton could lose second place to Vettel, and having Bottas in between them acted as a buffer to protect Hamilton.
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Vettel won his first title with Red Bull in 2010 after overhauling a 31-point deficit in the last six races, while in 2012 he took his third crown despite having been 44 points adrift of his then-closest rival Fernando Alonso at one point.