The problem with any form of suicide charge against the flood is exactly that: the flood don't kill you, they convert you. A pyrrhic victory against the flood spores is literally the worst outcome (aside from defeat) because then you'll spend even more resources on taking out your own prize fleet.
See the problem here is that you're assuming many of the Halycons will survive this engagement; as I think we can tell from all of the posts regarding the oldness and obsolescence of the Halycon, it doesn't really hold up well in pitched battle. Assaulting a Flood World is problematic for three reasons: 1. The damn Spore ships 2. Other infected ships 3. Flood-infected MACS. This basically produces an unholy clusterfuck of a bad time for any fleet that tries to take the planet. The use of massed Halycons is good in this sort of situation as they're tough as balls and their MACs outrange Spore ship's infection abilities. If you maneuver so you don't face too critical of a mass of Spore ships at once the Halycons are able to kill most of them quite handily while soaking up damage from the other forces.
Halycons are nice because they take up a low amount of population for the bang they give you, and they can take an ass beating and still keep shooting. I'd argue that they're one of the more useful UNSC ships against other UNSC ships merely because they in a way break the stereotype of the UNSC producing "glass cannons", they can soak up damage that would wreck a more expensive Marathon and ask for seconds, yet they take up less population. If you can manage to take an enemy fleet head-on with them they'll batter the poor bastards to bits... that said they're really quite vulnerable to strike craft seeing as they have no Triple A and are slow as balls; their lack of any appreciable speed also makes them vulnerable to being outmaneuvered.
Basically the Halycon is the cheap meat shield of the UNSC, and it does that very very very well in the right circumstances