My question on all this is how long would it really take to do a reroute?
The economics of moving the train are pretty clear financially -- the cost of refurbishing the SantaFe tracks are really high, compared to the ridership. And unfortunately, the SWC financial performance isn't in the same league as the Empire Builder or Coast Starlight. (I suspect the economics could be much better, with more capacity and strategic schedule tightening and shifts).
Right now, Wichita is somewhat served by the Newton station, located about 30 miles from Wichita. That station is reasonable - historic, ok parking, a bit frayed around the edges - but the train comes through in the middle of the night. Catching the train at 2:30am really isn't the most attractive option to most travelers. So the shift to get Wichita probably won't drive much higher ridership. If there were some way to improve the time to Wichita it would help ridership considerably, but unclear what impact that might have on equipment turns, utilization, etc.
Politics could be interesting. Several of the western Kansas towns served by the SWC have dumped considerable funds into station rehabs and used the train as a big plug for local development. Raton and the Boy Scout camp would really take a hit - buses vs. train really isn't that great of a change. Then again, Kansas' congressional delegation isn't exactly falling all over their selves to help get more funding for Amtrak, even in the good times.
I do wonder if this move happens, it would happen sooner rather than later - as the original article points out, the train transit time is up 10 hours since 1971, and it'll only get slower as more deferred maintenance piles up on the original route. If Amtrak finds itself under the gun on the budget, it's entirely possible they'll just say to heck with it, reroute, and let the chips fall where they may.