After some experimenting I found out that you can do the following in Project load script to achieve the same:
// Set script library
def header="Project ${project.name} load script:"
def scriptLibrary = context.expand('${projectDir}')+"\\soapui_groovy_scripts";
log.info "${header} Setting project Groovy script library to "+scriptLibrary
project.setScriptLibrary(scriptLibrary)
log.info "${header} project.scriptLibrary="+project.getScriptLibrary()
//Make sure global setting is cleared
log.info "${header} Clearing global script library."
com.eviware.soapui.SoapUI.settings.setString( "Script Library", "");
log.info "${header} Global scriptLibrary='"+com.eviware.soapui.SoapUI.settings.getString( "Script Library","default")+"'"