So I'm wanting to make a game to post on itch.io, but I want it to be embedded into the page and not be in .quest format. I've read a bit about the thing that converts .quest files to .js files, but it says its no longer supported. Any ideas on how to achieve this?

You could use iframe, but i don't know how.

If it's only Javascript, does that mean the objects will actually be exposed? I hope there is another solution

Upload to quest and set to private, then grab the url that points to your game and stick it in an iframe:

//<iframe style="src="https://play2.textadventures.co.uk/Play.aspx?id=youridhere">