Yes - read it. Chicken Little just enjoys worrying when there is little need to....but spin is important, right?

From the article "While providing an exemption for religious employers, the new rules maintain the existing federal contraceptive mandate for most employers." Note use of the word "most".

From your citation - " we anticipate that conscientious exemptions to the Mandate will impact a much smaller number of women..."
...and pay attention to the section where they analyze the numbers - around page 78.  Try "The expanded exemption for issuers will not result in a distinct effect on contraceptive coverage for women who wish to receive it..."

NPR - "HHS officials said they don't expect many companies to seek waivers. They said the group seeking waivers will likely be limited to those about 200 companies and nonprofits that have already sued."

WaPo - HHS contends "the change will still leave “99.9 percent of women” with access to free birth control through their insurance."