I'm not an expert in this race but I suppose that once the influence of the rather divisive Republican primary has worn off, Mourdock's numbers will go up. Republican Lugar supporters who now threaten to support Donnelly are probably going to cast their vote for Mourdock at the end of the day. Indeed, a similar development can be observed in the Republican presidential primary.
The main difference is that in the presidential election, most of those dissappointed Republican primary voters can't stand President Obama and only need to wait for Obama to say something that makes them mad before they will support Mitt Romney. Joe Donnelly is not President Obama. He is much, much more palatable to Republicans. Few Republican voters are going to get all wound up to go out and vote against Joe Donnelly.