The Minister's decision to allow Enmore School in Bridgwater to opt out from October 1 came after seven months' delay, and in the middle of the school term.
The authority sought an injunction but has now backed away from further legal action on the grounds that it would not help the school and that it would be an unfair burden on county finances.
Councillors have, however, called for independent consideration of appeals by parents about grant-maintained status.
Chris Clarke, council leader, said: "Present arrangements give enormous powers to the Secretary of State, who considers appeals against a process which is Government policy."
David Wicks, education chairman, added: "There appears to have been unbelievable rush and rudeness by the Department for Education and Employment in producing a panic timetable to increase the number of GM schools this month.
"I really do deplore the whole GM balloting process which sets parent against parent within the same school. Divisions are being created which take a long time to heal."