educate the users
but don't remove the option.
At my org where we use Duo approx 18% of the users (according to monthly Duo report) use SMS or Voice, about 65% use the Duo Push app(most of the rest use a duo generated pass code). This number hasn't changed over the past 6 months. At one point I noticed for whatever reason people located in what might be considered non 1st world(not knowing off the top of my head what constitutes 1st world) countries seemed to be more likely to use voice as the 2nd factor, at least in my org.
I don't expect Duo to remove the option, though I suspect their admin UI has the ability to turn off various forms of 2 factor if the companies wish to(I haven't checked).