That setting is not supported by JSChart: http://docs.splunk.com/Documentation/Splunk/6.0.3/AdvancedDev/CustomChartingConfig-AxisGrid#Numeric_...
That depends on the problem. As stated in your question, the solution might be "don't use axisX.minorUnit"... however, there probably is a more abstract problem to be solved that I don't know about.
and what's the sollution?