If you don't want to be demeaned, don't work in a job where your role includes cleaning up human excrement and vomit from trains.
Or, we as society could stop demeaning people for doing good work and making the world a better place. Do you want to be able to take a subway without the place reeking of shit and puke? Then be thankful for the people cleaning it up; give them respect, good working conditions, and a living wage. Anyone who is creating value for society deserves that much, whether they're designing the next iPhone or washing the piss smell of a public lavatory. And if you don't give them any of that, don't be surprised if they don't deliver very much value to you.
Besides, the demeaning argument could be applied to any kind of time keeping system. So you use your finger to clock on instead of a card. So what?
If the card is exactly the same, then why go through the expense of the fancy new equipment?
If the fingerprint system really is cheaper / more robust / maintainable / whatever, then it may make sense to upgrade. If, as I suspect, it is is more expensive, and they're doing it not to reduce costs and increase efficiency of processing but to have more control over people. Either that's not necessary, in which case it's demeaning, or it is necessary, in which case (it seems to me) they're doing something else really wrong.