The most important factor in the rise of segregation in the South was surely racism. There may have been other factors that allowed it to rise, but racism was the factor that caused it to rise. There can be no other explanation for segregation. White people believed that they were superior to African Americans and they wanted to ensure that they would not have to mingle with blacks on any sort of an equal basis. To prevent this unwelcome social contact, they imposed a system of segregation. They were happy enough to have blacks work as domestic servants in their homes, but they did not want to have to interact with blacks in any setting that implied equality.
Could things have developed differently? There is, of course, no way to know this for sure. My own feeling is that Southern society could only have developed differently if laws were imposed upon them by force. Once segregation was banned by law, Southern society started to change and the region is much less racist than it once was. This implies that Southerners could have changed if the North had imposed integration on them earlier. If the federal government had disallowed segregation after Reconstruction, white Southern attitudes might have started to change sooner and things might have been different at the end of the 1800s.