Unless you can convince your customers to send your larger amounts of BTC in a single transaction, no. Every payment you receive is going to be an input. There is a reason a lot of online services like gambling sites and exchanges have a "minimum deposit" value of around 0.001 or higher like 0.01.

Your other option is to try and find a payment processor who will aggregate smaller payments into a large payment to you... or do it yourself on a regular basis... every 10 transactions... collate them together, send them back to yourself with a low fee (use accelerators if they get stuck)... so you end up with a smaller number of larger value inputs.

It is the same issue that a lot of the so-called "cloud miners" are going to face soon... all these "daily payouts" of like 0.0001 are going to come back to haunt them now that BTC looks like it is going to stay $10K+ for a while.