The Tory former defence secretary told constituents he did not believe the move was a deliberate effort to "antagonise" party traditionalists.
But he said it was "a form of social engineering of which Conservatives should be instinctively wary" and would please only "a very small, if vocal, minority".
Dr Fox was particularly critical of planned legislation drawn up by the Government to allow same-sex marriage which he said appeared to have been written "on the hoof".
A legal bar on the Church of England performing such ceremonies - part of a series of safeguards designed to reassure religious critics - was "absurd and anomalous" when it did not also extend to the Catholic Church which had been still more vehement in its opposition, he said.
Prime Minister David Cameron has vowed to press ahead with a commitment to change the law by 2015 despite warnings the issue has caused widespread upset amongst grassroots Tories.
Dr Fox said it had already "led to the alienation of many loyal and, in many cases lifelong, supporters of the Conservative Party" and demanded a rethink "before things get out of hand".
He stressed he was not anti-gay and as a doctor believed same-sex relationship were "a variant of the spectrum of human sexual behaviour and should be treated with tolerance and respect".
But he said discrimination had been addressed by the introduction of civil partnerships and questioned the strength of demand for further reform.
"The principle of altering the accepted legal status of the majority of the population in order to satisfy what appears to be a very small, if vocal, minority is not a good basis on which to build a tolerant and stable society," he said.
"What makes the position worse is the way that the legislation increasingly looks as though it was made on the hoof to deal with the political problem du jour."
European courts could "drive a coach and horses" through the church safeguards, he warned, and it risked "weakening and splintering" Christians who already felt under threat.
"To fail to understand this is to risk an affront to a large stabilising and normally acquiescent section of this country which will sow completely unnecessary seeds of dissent.
"I do not doubt the sincerity of the proponents of this measure and think talk of attempts to purposefully antagonise traditional Conservatives is far-fetched," he concluded.
"However, I believe these proposals are divisive, ill thought through and constitutionally wrong.
"That is why I will vote against them in the House of Commons."