When I was consulting I helped a lot of small companies deal with this type of situation. We loved Stripe when it fit the clients need, but it doesn't always work out. First, you should reach out to Stripe support to see if you can fit into their micropayments model which means you wouldn't be paying .30 + 2.9%. You can also look at some of the other platforms that support micropayments, like paypal (although I hate paypal).
Outside of that, many times what we wound up doing was integrating to First Data or another local bank clearing house that would provide more proper low transaction fees. It takes more work and effort, but clients saved huge percentages of their small payments many times by doing this, so if you can't fit into one of the existing solutions you may have to do it the "hard" way. Nice thing about this is we usually could accept e-checks (ACH transfers) when doing this which also lowered the fees drastically and made things more profitable. There are rules of course on industries, types of payments etc, but mainly if you aren't doing anything "illegal", porn or financial services you can generally find a good clearing house through a local bank. First Data's api used to suck, no clue what it looks like today but it used to be a royal pain.