Moody's on Thursday said the proposal to extend that waiver until 2016 "will exacerbate the issue and will likely result in higher premiums for exchange policies with an insured population that will be less healthy and less profitable for insurers."
"Finally, the delay of the employer mandate until 2016 will cause complications for insurers and confusion for employers and employees," Moody's said. "Insurers have already begun to develop and sell small group compliant policies to employers. Now that these employers are no longer required to meet the requirements of the ACA for 2015, they may want to retain their existing policies for another year, forcing insurers to resurrect plans they had intended to discontinue."
When asked by CNBC about the potential negative financial impact to insurers directly from that employer mandate phase-in, Zaharuk said the change "is the hardest one to model out."
(Read more: What's behind AOL's Obamacare blame game)
He did say, however, that two more hypothetical changes to Obamacare worry both Moody's and insurers.
Those changes are extending the deadline for open enrollment in Obamacare policies beyond the current March 31 deadline, and suspending the tax penalty most Americans face next year if they do not have some form of health insurance by March 31 this year.
That tax penalty is considered a key motivator for uninsured people to buy coverage through the government-run Obamacare exchanges, and in turn to strengthen the risk pools of the plans sold on those marketplaces.
Republicans opposed to Obamacare have called for the elimination of the tax penalty, and some Obamacare supporters have called for extending the enrollment deadline to boost participation in the plans. On Wednesday, a spokeswoman for Health and Human Services Secretary Kathleen Sebelius firmly rejected the suggestion that HHS would consider either proposal.
Sebelius on Wednesday, in announcing that 3.3 million people had enrolled in Obamacare plans as of Feb. 1, noted that younger adults are now signing up at a faster rate than they had been. However, the percentage of younger adults who are enrolled is just 25 percent—15 percent lower than a target some experts have said is ideal for the plans' risk profile.
Zaharuk said the increased participation by younger adults in the plans is "good news."
But so far, it's not enough to offset Moody's overall negative outlook for insurers selling the Obamacare plans.
In its analysis last month, at a time when young adults comprised 24 percent of Obamacare enrollees, Moody's noted, "The demographics of those enrolling in individual products through the exchanges is a key factor in Moody's outlook change."
Aetna, when asked for comment on Moody's analysis, noted that "Moody's outlook for Aetna's ratings remain stable."
" Individual health insurance is a small portion of Aetna's business, representing approximately 3 percent of our 2013 membership and operating revenues," an Aetna spokeswoman said. "We don't expect our exposure to the individual insured business to change materially in 2014."
—By CNBC's Dan Mangan. Follow him on Twitter