The last thing the US and its partners want to see in Syria is a new post-Assad secular Syrian government. Assad has run a secular government for decades. Secular, in this case, really means nationalistic; that is to say, a government that would put the needs of Syrian people before the needs of the American Empire. Historically, when dealing with foreign nations, US governments have always demonized and attempted to remove leaders who showed any sign of not playing by American exceptionalist and expansionist rules.

A crate of Ukraine-made weapons at a Syrian 'rebel' base. The specified destination is Riyadh, Saudi Arabia. 

What the US wants is to choose who runs Syria after Assad is gone (if indeed he goes) because it can then pick the right person for the job of turning Syria into a US client state and 'open the country up to foreign investment'. Faced with a choice between a faction made up of real Syrians who have taken up arms against Assad and the CIA-trained Islamic fundie fighters, the US government will pick the fundies. This is as true today as it was 60 years ago. As noted by Robert Dreyfuss in his book Devil's Game: How the United States helped unleash fundamentalist Islam:

"During the cold war, from 1945-1991, the enemy was not merely the USSR. According to the Manichean rules of that era, the United States demonised leaders who did not wholeheartedly sign on to the American agenda or who might challenge Western, and in particular U.S., hegemony. Ideas and ideologies that could inspire such leaders were suspect: nationalism, humanism, secularism socialism. But subversive ideas such as these were also the ones most feared by the nascent forces of Muslim fundamentalism. Throughout the region, the Islamic right fought pitched battles against the bearers of these notions, not only in the realm of intellectual life but in the streets. During the decades-long struggle against Arab nationalism the united states found it politic to make common cause with the Islamic right."1
I am assuming here that there even are any 'secular opposition groups' in Syria that are fighting against Assad. I wouldn't be surprised at all if the only active groups fighting in Syria over the past 18 months are the CIA's Muslim terrorists.

A final point concerns the reference to CIA director Petraeus. As of yesterday, Petraeus is 'former CIA director, because he resigned, allegedly over an 'extra-marital affair'. Given that Petraeus was heavily involved in arming the al-Qaeda jihadis in Syria, and that he was ultimately responsible for the death of Libyan Ambassador Chris Stevens, because the 'embassy' where Stevens was killed was really a CIA compound and those who attacked the compound included Libyan 'jihadis' that Stevens had been using to send weapons to Syria, it seems that an affair was the least of Petraeus' worries and unlikely to be the real reason for his sudden resignation.

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1. Robert Dreyfuss, Devil's Game: How the United States Helped Unleash Fundamentalist Islam, Henry Holt & Company Inc, Feb 2006, p2