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You continue on through your cycle and don't worry about it. If you want to scrape them off the sides with a magfloat or something, go for it. But diatoms are a normal part of the cycle really.
Read this. The diatoms are only cleaning up the silica you have in your tank. This is a natural process in the aquarium and normally happens during a cycle because the sandbed is new.
I would by some animals (astrea snails, sand sifter star crabs etc) to start to mediate the nuisance Algaes. Had the same problem and threw in a reef cleaner crew from live aquaria and within several weeks BOOM crystal clear. I would get your water parameters a little more on track before u do that to limit the die off.