Hello,
Optimization algorithms for nonsmooth cost functions on manifolds is an ongoing research topic. And as Bamdev mentioned, there is nothing yet in Manopt to handle such problems (although Manopt was designed to be able to handle them when algorithms become available).
For now, typically we use smoothing (pseudo-Huber loss, for example), which has its pros and cons.
Sorry that we do not have a more complete answer at the time. If you find a good way to handle your cost function, we woud love to hear about it here, if you wish.
Cheers,
Nicolas