Thinking the York U station will stay open is completely unreasonable. It's tucked in the middle of an industrial park. Downsview Park makes a convenient connection that is two subway stops away, and still puts students in the heart of campus. The move may add a bit of time, but a small price to pay for co-locating the station within a major destination (the actual park). It will add TTC fare to the commute (the shuttle is currently free) but this a) emphasizes the need for the TTC/city to stop doddling and figure out integrated fares, and b) should be up to the university to address, since they will now save on a shuttle service and may want to look at assisting York U students/staff. All in all, it's just change, and people don't like change. Suck it up buttercup, this is Toronto, and change will never stop.
As for station configuration up the line, stations at Steeles and Finch would be subway spacing territory, even as we talk about RER. Another potential stop on the books is Concord (Highway 7), where it can be integrated into the viva rapidway. I don't think anything in between Concord and Downsview Park would be appropriate or entertained by Metrolinx, especially considering this is a regional rail service.