Eventually, yes.
Metrolinx's ultimate intent is to electricify all the corridor, and electrifation to Kitchener will also be required as an interim first step before
highspeed rail (under study). Metrolinx
owns most of the rail corridor to Kitchener now, the main gotcha is the CN-owned small segment. This is exactly why GO RER (phase 1 electrification) stops at Bramalea for now, but multiple solutions are currently in the works (Metrolinx is currently negotiating with CN for electrifying into Brampton and Mt Pleasantville, and if that fails, there are possible alternatives such as the
Freight Bypass). Once this is done, sooner or later, there's no stopping SmartTrack trainsets from reaching Pleasantville eventually, and then Kitchener. Depending on trainset selection, of course, and the demand for traffic. Obviously it would not run every 15 minutes to Kitchener with current population, but hourly 2-way electrified service within 25 years sounds feasible.
The other fly in the ointment is the use of lighter (non-FRA) trains, such as the Stadler KISS (which Ontario, GOTransit & Metrolinx is now very
frequently pictogramming -- The pictogram might even be the SmartTrack train). Transport Canada restricts lighter trains on heavy-rail corridor, but Transport Canada has
communicated flexibility which keeps the door open. Transport Canada would force requirements to permit lighter SmartTrack trains on GO network (e.g. full grade separation, and perhaps
Positive Train Control) before allowing it to happen. This is not saying it will happen, but the door is definitely open,
especially if politically accelerated.
(drum roll.... look at Thomas Mulcair's love of trains -- including high speed trains, choo, choo!).
If such a train is chosen, it won't be allowed to go to Kitchener if only the Bramalea-Stoufville section is made compliant. At least until corridor megaprojects (e.g. for HSR) occur all the way to Kitchener to make the corridor comply with any Transport Canada waiver for the SmartTrack trainset (if one is given).
In this case, the SmartTrack EMU would cover the core segment, while electric-locomotive-driven bilevels would go beyond the SmartTrack endpoints -- at least initially. But the Bombardier BiLevels will eventually wear out in the coming decades. Metrolinx will probably only replace them with electrics. Eventually, SmartTrack trainsets could reach Kitchener -- albiet long after electric-locomotive driven 12-car bilevels have been running for a long time.
Then again, accelerated high speed rail plans in a future government change may cause bilevels to be reallocated away from the Kitchener-Stoufville route sooner than later (to run only EMUs). Lots can suddenly change.