Your concern is understandable, non-contiguous selections have been dropped from v3.
Either you can use checkbox selections or add this code to unselect rows with ctrl key.
rowClick: function(evt, ui){
if(evt.ctrlKey){
var isSel = this.selection({type:'row', method:'isSelected', rowIndx: ui.rowIndx});
isSel && this.selection({type:'row', method: 'remove', rowIndx: ui.rowIndx});
}
},