So, this is a lot of 'my bad' moments and I'm not feeling like the friendliest owner right now. :'(

I have a budgie with a history of health problems, and she has been mating with another of my male budgies on and off. This was fine, I just did what I could to discourage nesting habits, but my female budgie, Mac, would continuously end up in my dresser drawers. We blocked them up like we did every other nesty corner of their free fly room, but she was very persistent and managed to get in a few more times.

I have had a female budgie have a full clutch before so I do have some very beginner experience with the breeding process, and I recognized Mac had an egg-butt eventually. I was really worried she might become egg bound or something, it looked like there was an egg coming no matter what I did. So, in order to avoid something serious like becoming egg bound, I filled her diet up with calcium and let her make a nest.

I took the eggs from her within the day of laying them, and doing more research felt that I shouldn't be encouraging her egg laying anymore, as she's not going to want to stop until she has babies... So I'm mostly unsure what may be more damaging to her-- letting her continue this clutch, or just trying to continue with discouraging egg laying, despite her clearly having an egg growing?

Any advice would be awesome, and thank you in advance <3

For the sake of your female's health, she really needs to be prevented from mating/breeding with any male in your flock.
Only you can ensure that this behavior is prevented.

First, I recommend that you separate the female from the male totally.
Put the male(s) in different cages, in a different rooms from where you house the female(s).

Make sure you are rearranging the cage of the particular female that has been mating every couple of days.
Rearrange everything in the cage - perches, toys, food and water dishes, etc.
If possible, move her cage from location to location in the room and/or in the house.
Do not allow any of your female budgies to have a nest box or anything that can be used as a nesting site in the cage.
Allow the female(s) to have out-of-cage time ONLY when she is under your direct supervision so you can ensure she is not going into corners, drawers, etc. where she might make a nest.
A couple of hours a day is sufficient for out-of-cage time.
Remove all eggs and dispose of them immediately.

Keep in mind that a budgie lays a specific number of eggs each cycle.

The first week the hen's body is preparing to lay the eggs.
The next two weeks is when the eggs are laid.

If a hen begins a cycle and you remove the egg(s) and start action to break the cycle, she will often continue to lay until the changes in the environment trigger her body to stop.

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thank you so so much for the advice, I will work on doing this all right away!!!

You are very welcome.
Please let me know how things progress.
Best wishes!

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Good luck, and definitely take this seriously. My girl Lemon passed away after years of egg problems. I'm not saying this will happen to your girl but it is a possibility.
You can do it!!