Yes, in context, the "them" he refers to is "man and woman", But that still leaves the problematic bit about man and woman being male and female "at the beginning of creation." IOW, human beings were in their current form at the beginning of creation, which I think implies that they didn't evolve.
And this bit's central to Jesus' argument, so I don't think it can be brushes off as easily: he's saying that divorce (at least the particular system of divorce that Jesus refers to) is contrary to the model of marriage that God established right from the start, and God's intent was for married couples to stay together for life, so divorce should be avoided.
Whether he means it means divorce should be avoided altogether or whether he means that people should take marriage more seriously than those particular people were is probably a matter for discussion, but Jesus' whole argument is based on this idea that marriage for life is the "original" model, which implies that men and women were "originally" there.
There's only one possible "out" I can see: if the words here allow for some alternate phrasing like "... in the original design" instead of "... since the beginning of creation", then that could allow for evolution and be less obviously wrong. I just don't know if the original text actually supports it, though.