Agree with having a higher tier(one that wouldn't bill ebike by the minute).If ebike utililization drops off a cliff, maybe they will revisit the incremental charge. If the problem was a small group of users camping on these, this seems like a good change to make sure they are broadly available. Maybe there are other structures that could work, such as a higher fee membership that includes 2x30 minute ebike sessions per day, and each additional session costs per minute. This would serve the same purpose of discouraging gig workers from monopolizing them.
Really, gig drivers would/should be better off renting their own ebike, not using a bikeshare. There are services that offer long term ebike rentals. I guess Bikeshare helps to reduce risk/liability of theft.
Your idea if of capping the ebike use per day then charging by the minute if you go over your cap is an excellent idea.
As an aside, I've only used the ebike once. The only time I think I would really need it is if I'm going uphill.