Pseudo-temporal ordering in heterogeneous populations
Regarding the first part of the question: scRNA-seq is a rapidly developing field so it may be hard to talk about "widely accepted tool for doing pseudo-temporal ordering from scRNAseq data". Few of the tools aiming to do just that include Monocole, Waterfall or Sincell (see this paper for references https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122333/)

The second part is a bit more complex. Many aspects have come together here, e.g. cell-cycles, sub-populaitons identification and pseudo-temporal ordering, to get a true reflection of the biological processes. There are efforts on all (and more) these fronts (see again e.g. the above paper, though not the latest) and there are most likely people working on their integration. I'm not aware of any studies published yet at this depth though