I agree with you completely about the crew problem. I think MARC is large enough now to start thinking about having their own employees operate trains, like other rail services in the Northeast.
I don't think getting Delaware to pay will be a problem, nor will the relatively small number of passengers. Remeber MARC already has a successful contract with West Virginia (2 round trips daily+ 1 evening express) and the MARC trains headed to Martinsburg are the busiest and longest ones on the Brunswick Line. I would expect the number of commuters from DE to BALT/DC, plus the passengers from Elkton (where a station would definitely built before the extension), would be much greater than the number of riders from WV. I also would expect that the MARC Penn Line/SEPTA R2 would capture a significant share of PHIL/BALT/DC intercity trips, similar to the NJT/SEPTA share of NY/PHIL intercity trips. I don't think anybody has the time or patience to travel between New Haven and Washington solely by commuter rail.
I am also pretty sure that MARC would not operate express service between Newark and Baltimore; local service between Newark and Baltimore then
express service to DC is more likely.