All you need to do is hook up to the headerCellRendered event of the igGrid and in the handler consider the ui.columnKey param.
Thus you can apply the text justification only to the desired columns.

Here's a code sample of how to accomplish this:
(I'm attaching a working HTML page that illustrates the sample code) 

$("#Grid1").igGrid({
     autoGenerateColumns: false,
     dataSource: sourceData,
     primaryKey: "ProjectID",
     columns: [
        { key: "ProjectID", headerText: "Project Id", width: 100, dataType: "number" },
        { key: "Name", headerText: "Name", width: 200, dataType: "string" },
        { key: "StartDate", headerText: "Start Date", width: 150, dataType: "date" },
        { key: "EndDate", headerText: "End Date", width: 150, dataType: "date" },
        { key: "IsPostponed", headerText: "Is Postponed", width: 100, dataType: "bool" }
    ],
    headerCellRendered: function(evt, ui) {
        if(ui.columnKey === "Name" || ui.columnKey === "StartDate")
        {
            $(ui.th).css("text-align", "center");
        }
    }
});

Cheers!
Borislav 

Hi guys,

I'm afraid that the only reasonable solutions to this are the ones that Angel has provided in his posts.

Due to reasons I'm afraid that we haven't had the opportunity to provide an easy-to-use out-of-the-box solution (although cell templates will work perfectly in such a situation).

If you wish to submit this as an official feature request, you can now do so from this form: https://es.infragistics.com/my-account/feature-request