I am sooo jealous of your attic Julia!
Ok, manure can smell, which can be an issue. If I were you, I would not seal the entrances of the bats, but I would seal the bottom of the attic, so it doesn't smell downstairs.
Then I would use the manure in the garden, and enjoy the pest control they provide: They reduce the mosquito population to a point where malaria was eliminated from Texas (see link below).
Some studies have also found that having bat colonies around maize fields could provide enough pest control to avoid insecticides.
Moth species which are pests in maize are not only eaten by the bats, the ultrasounds bats make are also pushing them to hide, and starve instead of infesting new plants.
For this reason, many ecological farmers would be very envious of your bat colony in the attic, and are even building homes to try to attract them.
Did you know that bats around the world are threatened by a new fungal disease? In addition to that, their populations decline due to habitat loss, less and less hollow trees, attics are shut, etc.
https://www.notechmagazine.com/2018/02/biological-pest-control-bat-towers.html
Now about the health issue: Bats
can be hosts of some diseases. This is due to their temperature being higher, so they survive diseases which are dangerous for humans. However, not all bats carry these diseases.
It would be the same as killing all beavers in Britain because they could get a certain disease. Or killing all chicken and cows because we could get bird flu.
To avoid these diseases, you can wear a face mask when working in the attic, change and wash your clothes and shower after working upstairs.
Which country/region are you located in? There might be some bat protection group supporting you with your struggles.