I think the strongest argument for preserving the conference alignments is that it builds rivalries.
When teams are slotted by conference, they are much more likely to match up with each other. This creates great dynamics like the Celtics/Cavs series of the late 2000s, or the Celtics/Pistons series in the late 1980s, or Detroit/Chicago a few years later, or New York/Chicago...or countless others where an up and coming team needs to "get over the hump" by beating the same team it's lost to for the last few years.
I'd argue that over the years, these have been the most compelling playoff series to watch. In fact, I'd say that these repeated matchups are the essence of what makes NBA playoff basketball great.
If you took away the conference/division structure, matchups would be more haphazard and you wouldn't get the same year-to-year persistence that leads to the truly storied pre-Finals series.