I think Kennedy between Lawrence and Ellesmere is due for a widening anyway, might as well start that now and put in permanent carpool lanes similar to the system on Eglinton, Don Mills, Yonge, Dundas, (formerly) Dufferin. But if traffic still seems to interfere, make them bus only till the end of the project. Remainder from Lawrence to Eglinton would be left alone.
Another idea would be Between Ellesmere and Eglinton, Widen Midland and Kennedy to a 5 Lane cross-section throughout its entirety. Then during the shutdown, there will be 5 lanes, 3 Northbound on Kennedy and 3 Southbound on Midland. Buses would have a reserved lane on both roads. Once the shutdown is complete, these 5 lane roads can turn into 4 lane + bicycle lane boulevards or 4 lane + middle turning lane. Either way there is a short term and long term benefit.
Another option that is quite obvious is... Create a new Ellesmere and Lawrence branch of buses, Lets say 54S and 95S. These two routes would be local along their respective routes and then once they pass Midland, they travel express straight to Eglinton Station?
Also, how about an express point-to-point service from Kennedy to Scarborough Town Centre? Most commuters travel between those two stations in the first place. Can the TTC invest in 60 Ft buses between now and 2015 specifically for this shutdown?
Despite all these recommendations, my vote still goes to accepting TTC fare on the GO Train between Kennedy & Agincourt.