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You can. It won't necessarily hurt, and an advantage to keeping it around is that eventually there isn't going to be any more food available for it to keep reproducing. Personally, I don't mind algae so much on certain places. But diatoms can be a bit unsightly. If you think it makes your aquarium look dirty, then you can clean it up to suit your own aesthetics. For a betta, there's really no advantage to keeping the diatoms (unlike some other fish, which might eat some of it). And, if the diatoms die for any reason (intentional or otherwise), then you have a new contributor to the bioload.
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