Yes, it would depend on how late it is and where it lost the time. A week ago they bussed all the way from El Paso to Fort Worth when the Sunset was running about 13 hours late by El Paso. Those were some exceptional circumstances, but the answer really is... it depends.
I've had a 6 hour layover in Minot on the westbound Empire Builder before. The eastbound was late due to a derailment, and the crew needed their required rest time before heading back west. Without knowing if the prior eastbound was late, I can only speculate that this could be similar.
You also have the option of public bus service between Newark and the Wilmington station on Friday evening. Look for routes 6 and 16 at: http://www.dartfirststate.com
Unfortunately there isn't Sunday service, but it sounds like your return train will work out.
The Railfan & Railroad article was very good. Unfortunately, the passenger service just wasn't practical. Driving was quicker, flying was half the price, and the government just said no more. The dinner train (one of the fanciest and best run operations around) was only part still making money...
Sounds great, the line certainly needs it (esp. on the shared SEPTA portion). I wonder though, will the fares double as a result? In comparison to travel on the corridor, Harrisburg has always been very inexpensive.