More likely than not, Fuddy is possibly connected to BHO via the Subud Organization. Loretta Fuddy acted as the Subud USA national chairperson from 2006-2008, while she was based in Seattle. (Offices in Seattle, Chicago, Honolulu and the DC area, among many other locales.) Stanley Ann Dunham (SAD) was said to be a member of Subud while the Soetoro family lived in Indonesia. The strongest single link for that thesis may only be a picture of a Subud meeting in which Dunham is claimed, inconclusively, to appear (back row, fifth from left). 
SAD, however, was also known to live in Seattle, where there has long been a Subud House, a mere nine-minute walk from where Dunham lived. Fuddy may have been a friend of SAD and conceivably could have been an acquaintance of SAD's mother, "Toot".
Thus, 1) possible Dunham picture at a Subud meeting, 2)Dunham lived 9 minute walk from the Seattle Subud house, 3) "coincidence" of former Subud chairperson Fuddy's appointment to a position tasked with procuring BHO's certificate. 4) only 5-year age difference 5) Indonesian intersection for both Subud and Dunham/BHO. Conceivably, BHO could have met Fuddy in Seattle.
Dunham and Fuddy were said to differ 5 years in age, with Fuddy being the younger. Dunham did receive a doctorate in anthropology. Though the Director of the HDOH was customarily a medical doctor, Fuddy does not have such a degree. One website (1 below), refers to Fuddy as "Dr. Fuddy."
In the '60's, then-President Sukharno called the Subud out publicly as a CIA-front organization. Suharto overthrew Sukharno to become Indonesia's second President in a bloody 1965-67 coup that left half a million people dead. It has been noted that Lolo Soetoro was (or would become) a high-ranking military man in support of Suharto after Soetoro spent time working on a degree in geography at Honolulu's East-West Center (which has been possibly linked to the CIA 2) and where he was said to have met Dunham.
After experiencing Toot's death just before he took office, there may have been suspicion surrounding Obama concerning anything that might be considered a politically-motivated death. BHO notoriously said May 15, 2013 "we're gonna punish our enemies and we're going to reward our friends who stand with us on issues that are important to us." There could be no more loyal friend in that context than Ms. Fuddy. If there were another (actual) death (that could remotely be considered a murder) among the crowd that otherwise fit BHO's "friend" category, there might well be repercussions that would keep BHO's operatives from being as loyal as he would certainly want them to be.
Fuddy knew "where the bodies were buried" (figuratively). She may well have kept the LFBC procurement issues all to herself, perhaps even as insurance for just such a circumstance as her exit from public awareness. If she were gone, and someone started apparently proving they were involved the forgery, who would know otherwise? With Fuddy alive in the background, he can separate that wheat from chaff for anyone that might otherwise think more voices need to be silenced (unnecessarily).
Fuddy was involved in a number of shady document forgeries. The same reasoning would apply to possible undesired disclosures there.
Twenty days before the crash, Sheriff Joe and the CCP were claiming to have "universe shattering evidence" of which the Deep State had surely long been aware, involving the Intelligency Community, Dennis Montgomery, and "The Hammer." Fuddy almost certainly would have been in on all that. Her mindshare would not be a good thing to just snuff out.
Similar to what you said, I would agree that anybody who can plant a $2B submarine nearby as its divers wreak minor mayhem can fix an autopsy as easily as a parking ticket. The book discusses that all in needed detail, however.
I don't think she'll tire of exile, knowing the Toot example. With a makeover, money, and surely several other Catholic church choirs to visit, she could be good for a long time.
What I think you're missing, however, is that she is a member of the Deep State, not some external pawn. Other Deep State folk would watch what really happens to her as an example for their own care/life under the system of the elites. Expense? Are kidding? Did you not notice that P&WC coughed up? Any need for replenishment there could be accomplished in a single line item on an otherwise-unnoticed government contract.
Too complicated? Did you not notice the calling cards of the submarine and a swapped engine? Nothing is too expensive or too complicated. They're proving to any spook, insider or wannabee that there's nothing they can't wave their magic wands to do. They work out of bravado, not out of fear of being found out.
So, all-in-all, why not let her live and keep the possible benefits of knowing important information rather than needlessly snuffing it out? Other friends of Barry would be happy to know the Deep State didn't kill her and thus, continue to carry water for Barry, where an actual killing could have seen intelligence dry up. I think the video may well have been commissioned to be able, in part, to "prove" no one killed her. Fuddy's assistant would appear to take the blame, as he said she died shortly before she drifted away from him." (How he could let that happen, supposedly without calling for reinforcement from all the other plane occupants is inexplicable to me, but we already know Fuddy had exited the area while everyone was still around, so that part just never happened.) But the assistant had Father Killelea vouching and speaking for him on camera (lest anyone see through the assistant's body language, I suspect). (The assistant also was allowed to see his lawsuit settled "favorably.")