First off, I think we should dispense with the notion that the biofilters are exclusively jizz. If Janeway’s in the middle of one of her period dramas after her third cup of coffee that morning, and she needs to drop a massive deuce, does she pause the program, or hike up her skirts over a chamber pot in the corner like a proper Regency era governess?
And you want them to use the transporters to beam waste material around the ship? The system that created Tuvix?
In “Day of the Dove” Spock claims that intra-ship beaming is dangerous, “Pinpoint accuracy is required. If the transportee should materialise inside a solid object, a deck or wall,” and in “Twisted” B’Elanna has to specifically configure a transporter for site-to-site beaming.
(please ignore season one of Disco, where characters just tell the computer to beam them somewhere on the ship, and it does so instantly without issue)
Not to mention that page 108 of the “Technical Manual” cites that site-to-site beaming requires double the amount of power expenditure, because it is essentially two transporter functions combined into one.
When you get right down to it, having the lower decks change out the biofilters just makes good sense. And what else are they doing while bridge crew actually handle all the important jobs? I’m pretty sure ensign Jones will survive if he misses this week’s life drawing class or poetry recital.