There is still a lot of controversy about the Dead-Sea Scrolls, but mostly about the nature of the people who wrote them. It was initially assumed that they were a cloistered, hermetic community called the Essenes but more recently there's been evidence of a far larger community, including both wealthy women and prostitutes, suggesting a vacation resort.
Of course it may have been both, at different times - a remote group of self-exiled religious zealots at one time and a playground for the wealthy another. Finding out about the authors of these scrolls is important because they may be the scribblings of a remote extremist sect that had little or no impact on Judeo-Christian history or they may have been stuff that had a mainstream impact. Simply said, we don't know enough just yet to say.
As for the challenges to Christianity, that was what many feared when the scrolls were first found, that one of the scrolls would have something like Jesus extolling the virtues of prostitution or worse yet, saying something like "Believe in no church." Luckily, that hasn't happened and while there has been some contradictory things mentioned in them that is par for the course with any sacred scriptures. When the Church first decided to utilize the new technology of a book binding to create a canon - the Bible - Church elders had to sort through multiple versions of texts with sometimes contradictory versions of Biblical stories and decide which was the authentic. The Dead Sea Scrolls have so far helped us understand the Biblical era moreso than any particular aspect of the Bible. There has been a lot of secrecy surrounding the Scrolls but that is due to academic rivalries and not Church conspiracies.
