What are her likely plans for sixth form?
If she intends to do maths (and even further maths), and will be continuing at a school where most students have done the further maths GCSE, there's an argument for continuing in the top set. However if she's dropping maths, or will be going to a sixth form where not everyone has had the opportunity to do further maths, you're right that she doesn't need it.
However even in the latter case, be guided by her maths teachers, and perhaps see how this term goes. If she's really good at maths, she may catch up easily. (DD did no maths during the first lockdown for mental health reasons, and it did her no harm). Some of the further maths material will revise/consolidate the GCSE stuff.
With science, is the set-up that the top set do triple in the same time as the others do combined, or do they have additional timetable time for triple? If the former, there's no time gained within the timetable by dropping down, so it's only the revision time.
I think there's much to be said for seeing how things go next term, and deciding later. If it gets to mocks and one option is looking much weaker, that would be the time to drop that to concentrate on others. (Something to check out is whether the mocks are on everything covered so far. For instance, they may have tested the year 10 Eng Lit texts last term, and just set a paper on the new texts next term; if so, she ought to have a go at the year 10 paper as well, to measure how she's doing on those too.)
The biggest problem is going to be the "set on level 9s", and the effect on her mental health if that's not going to be possible. You may need to find ways for lower grades to be "okay". In some ways, reducing subjects to give more time means there's less "excuse" in the others, putting pressure on in a different way. Talk to the school about this too. DD's school gave her very high "minimum target grades", so that on every report she was failing to meet some of them. If your DD's school do something similar, I'd hope that they might revise some of the targets in the light of her absence.