timing wise, it takes roughly 25 minutes on the subway from Main to Union. Longer if you need to wait for another train at Union to pass before getting on the yonge line. 10 minute trip time from Danforth GO to downtown on the GO train, so even if you gave yourself 10 minutes to transfer, you would still get time savings. according to twitter its roughly a 5 minute walk to the GO platform from the subway, so giving yourself a 10 minute buffer to get there should be plenty. (time leaving your house so that by the time the subway gets to Main you have 10 minutes to get to danforth).
As a frequent user of Stouffville, they can fit a few more people standing at Danforth. Its going back that may be an issue as these new danforth riders will be "stealing" seats for the 10 minute ride from existing users. GO transit crowding levels are never horrible, and in the end can handle a bit of a higher load for short inner city trips like this.