Formally yes, practically no.
Although religious practice is nominally free in France, with a completely secular state that does not interfere in religious beliefs, there are mechanisms that could be used against "dangerous" cults which threaten rule of law, especially if said cults endanger human life. Therefore, theoretically, the French state could act against the Islamic community if it does not disavow parts of Islamic doctrine that call for violence and killing of unbelievers.
But in practice, non-Islamic government could never be authority in Islam, and even Islamic scholars could not simply erase over hundred verses in Quran that call for violence. In fact they could not erase single one. What would probably happen would be employment of Taqiya-lying to unbelievers, where official leaders of Muslim community in France would publicly claim lots of thing like aforementioned verses in Quran are no longer valid, how Islam is religion of peace etc... Butbut inside the Islamic community violent parts of the Quran and Islam in general would still stand because none has right to change ostensibly words of Allah given to Prophet Muhammad.
Therefore, it is absolutely clear that any reform of Islam started by the secular French state would inevitably fail.