The scale chosen there is based on the histogram:maxBars advanced config setting. If you raise the limit to 3600 then you will get a true per/second count as long as your date range is less than or equal to an hour. Any more than an hour and it will keep scaling. Of course, you'll likely run out of pixels to render bars if you take it any higher than about 1000
Timelion might be able to do what you are looking for. It has a function named scale_interval(), which allows you to scale the value based on the with of the interval used in date histogram aggregations. If you e.g. are plotting request rate, you can display this as requests/second or requests/minute no matter what the aggregaten intervall is. This is tracked in the following GitHub issue.
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