After Effects sees an image sequence as video just like any other video. Get the hyperlapse imported, color-corrected, stabilized, and flicker-reduced, then precomp it and do a 3D camera track. After Effects should do it with no problem, although it's likely to be a loooooooong analysis time since, unless you downscale and render out an intermediate file, it will be very high resolution.
I've done one short test and was unable to get a track to work. But that may have been because there just weren't enough frames for the amount of motion (I rushed it and made the space between shots pretty long).