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I am a Dhoni fan but this particular incident was a dick move from him, normally captain gets a 100% fine or worse match ban when they deliberately rig the gameplay.
In the past, many captains faced the consequence and were slapped with the fine for less but he's powerful enough to influence even the match referee.
Ravindra Jadeja, Deepak Chahar and Maheesh Theekshana already bowled their quota of overs and MSD wanted to bowl Matheesha Pathirana as he has 3 overs left in his quota and he only used the loophole that was available as this was the first warning by umpires even if they did that and only then they umpires could award the opposition team with 5 penalty runs for the delay and from what i understand the umpires even did not consider that situation.
If Hardik Pandya opposed the move then the match referee could have taken the action like you mentioned, do you really think that any players who played under him will raise any complaint against MSD.