There can be many beginnings, but Mark’s version of this saying is more specific, “from the beginning of creation” (10:6). So, how should we understand “creation”? Is creation an event that took six days? If so, the beginning of creation would be the first day, or at least surely not the last day of creation. But according to Genesis 1, it was only on the last day of creation that humans were made, male and female. Since that reading leads to Jesus saying something obviously wrong, perhaps we shouldn’t understand “creation” as referring to the entire creation event.
The context of both Matthew and Mark’s versions of this saying is divorce, a decidedly human activity. And Jesus is referring to what was made “male and female,” which is not rocks, bacteria, bees or dandelions. Jesus isn’t talking about all creation, he’s talking about humans. If we interpret this saying as speaking about human creation, it makes a lot of sense: our Creator made us male and female from our beginning. Science has no disagreement: there never was a time when humans existed without being male and female.
The trouble, perhaps, is that once the verse is interpreted in a way that doesn’t contradict Genesis, it also doesn’t contradict mainstream science. But should that really be a problem?
I don’t see anything about a global flood in that passage. If you think “swept them all away” could only mean a global flood, do you also think “destroyed all of them” in Luke 17:29 speaks of a global cataclysm? I think Luke’s parallel shows that Jesus had no problem using regional events to speak of what the day of his coming would be like.