Bone admitted he didn't know the extent of Boyle's illness, but said he had seen "many, many" swimmers fight back against the odds.
"They overcome adversity and they do it in spite of [illness]... You have to look at the campaign that she's had. Swimming New Zealand has given her everything that she's wanted - the opportunity to train offshore, all the resources. I'm disappointed with the fact she swum, I guess, as badly as she has done. She's certainly a lot better than that and has proven on the international stage she can handle it."
Preparing for an Olympics is totally different from a world championships, Bone said, because of the attendant media hype and public expectation.
"No one will be hurting more than Lauren will be. She'll be bitter with herself, she'll be angry and twisted but, at the end of the day, they're disappointing swims.
"Her 400m New Zealand record [time] would have got her a medal. We haven't had the 800m final yet but the kid is going to be extremely disappointed and we don't know whether she's going to go on from here."
Boyle has cut a disconsolate figure in Rio, saying after her swim this morning: "The swim was better but I'm not strong. It's gutting."
Boyle was not the only target of Bone's disappointment. He said the experienced Glenn Snyders did not come up to scratch, either.
"Yes, he made a B final in the 100m breaststroke but he'll be disappointed he didn't go under the minute. That's what he would have been aiming for."
There was more cheer in the performance of youngsters Corey Main and Bradlee Ashby, who recorded personal bests in their events.
"Generally, swimming a personal best out of New Zealand will put you in a position to make a semifinal. That was important for Main and Ashby. It's a significant result. Does it make it great? No. We want to be in the top eight.
"Is it good enough for Glenn Snyders and Lauren Boyle? Absolutely not."
Swimming received $8.5 million in high-performance funding during this Olympic cycle, $5.6m of that in core funding and the rest in grants paid directly to athletes. Comparisons with canoe slalom ($940,000) and shooting ($101,000), sports that have brought home silver medals, make for ugly reading.
New Zealand has not won a medal in swimming since Danyon Loader's double gold in 1996 and Bone said he fears for the future funding of the sport.
"If Lauren Boyle retires that is a lot of high-performance money that's going to go because huge amounts went into her campaign, along with Glenn Snyders.
"We have some young swimmers on the verge. I'd hate to see the funding dry up in its entirety because we have to look at the future."
Swimming, Bone said, had more fundamental problems than just poor Olympic performance.
New Zealand lacks the critical talent mass to produce stars to replace the likes of Boyle, Moss Burmester and Loader. It also lacks the coaches with skillsets to turn talented youngsters into world-class athletes.
Most worryingly of all, there was a lack of good pools for swimmers to have access to.
"There's no doubting that," he said.
