I found the Stripe Plus Gateway - It looks promising and initial testing looks like it uses Stripe properly
Seems to be somewhat more updated. I unchecked the "process payments unsafely" in Stripe, set this up and it's able to save credit cards (test) and process payments. It appears to be done quite well.
I perfectly fine using a 3rd party gateway especially if it's more up to date. Also could this help the Blesta devs implement it as a solution? Because it doesn't look like @Cherry rewrote the whole payment system, just implemented the Stripe gateway as it should have been done in the first place.
I haven't dug into the code or anything to see how it works but this is looking promising again. My only worry is using this gateway and some day converting back to the blesta gateway and having trouble linking up tokens, etc.