There seem to be a lot of fans who are under the impression that Fi was intentionally made to be a slave within the Master Sword. And that this is partly why some hate Hylia. Because they think that Fi is a slave against her will.
But this just shows how little they know about Japanese culture. At least in regards to weapons or even just tools in-general.
You see, from what I know, the Japanese have a very strong tool & weapon maintenence culture. Where they will repair & repair & repair a tool/weapon until it literally cannot be repaired anymore. To such an extent, in fact, that they even have burial mounds for them when they can't be fixed anymore.
In fact, chefs will sometimes pray at mounds of kitchen knives in the hopes for better skills at cutting & cooking. And I'd assume similarly for other tool/weapons mounds as well.
They respect their tools & weapons very deeply.
Part of the reason for this is due to the belief that when you used a tool/weapon enough that a spirit will begin to dwell within it. As such, they treat them with deep respect.
This spirit is known as a Tsukumogami (付喪神, Tool Kami or Spirit) & is thought to make it a part of the owner, an extention of them even. Which, itself, is thought to make it more effective as a weapon.
And, seeing as Nintendo is a Japanese company, it's very heavily likely that this is the inspiration behind Sword Spirits to begin with.
So, it's unlikely that Hylia legitimately made Fi, specifically with the intention of turning her into some sort of slave, so much as Fi came into being as a direct consequence of being a Divine Blade, which itself might've simply sped up the process of the sword obtaining a spirit. Perhaps Divine Objects simply have spirits by default whereas mortal ones take time to develop them?
If so, then it is in her very nature to be a part of the sword. It's natural to her. We just don't understand it & probably find the idea alien.
In fact, if she were to be "freed," not only would it most likely lessen the Master Sword's power considerably, but she'd likely not even understand how to live separate of the Master Sword.
She could possibly react to it similarly to how Amalthea initially did to being turned human in the Last Unicorn.
Basically, it's not that she's trapped inside the sword, so much as she is the sword. It's her body. It's not Fi... & the Master Sword so much as it is Fi, the Master Sword. As in, the Master Sword's name is Fi.
The being we think of as Fi, in all honesty, is likely just a projection of the Master Sword's will for SS Link's benefit more than her own.