Nope. There are trains every 15 minutes in the peak period/direction on the Lakeshore East Line (plus VIA trains) between Guildwood and Rouge Hill. There are no plans to grade-separate those crossings. The same between Dixie Road and Southdown Road through Mississauga. We could also mention LRT lines in Calgary and Edmonton that have plenty of railway crossings with 2 and 3 car LRT trains operating as frequently as every 5 minutes. Or the outer ends of Chicago's Pink and Brown Lines.
I don't see the immediate justification for grade-separating minor the crossings like Mill and John Streets in Brampton, Scarboro Street in Malton, Revus Avenue in Mississauga, or Galloway Road in Scarborough, even if you run more frequent trains.
It's possible to operate such service, but there's a big distinction between streetcar-sized LRTs and massive 12-car bilevels, which probably will continue to run Lakeshore RER (electric locomotive driven) swallowing up the newly ordered Bombardier coaches/cabs, even if the route that need EMU benefits the most (Bramalea-Stoufville with "SmartTrack" infill stations) convert to a new trainset. Also, upgraded 15-min 2-way can mean crossings on both sides around every 7.5 minutes offpeak. During peak, it could be even more frequent. For the huge bilevels, grade crossings need to close earlier and longer, than they would need to for a slower 1-car or 2-car LRT. Accidents at level crossings have been a thorn on GO Transits' side from time to time, and increased service typically comes with increased accidents. Also, if they dead-head lots of non-FRA trains to the Whitby maintenance centre, we might need to physically separate GO RER from the road network.
From what I see:
-- RER electricifation won't reach Mill/John streets. Less urgent until RER reaches Brampton, and/or HSR gets approved.
-- Scarboro grade separation is actually planned (unless that's cancelled), drum118 mentioned this too, so RER Bramalea will likely be fully grade separated. Also, concurrent 15-min RER and 15-min peak diesel, excluding other services (i.e. VIA) can mean grade crossing is closed longer than open during peak period, given the required at-grade closing length.
-- Galloway Road, and many Lakeshore East level crossings are trenchable (minimizes expropriation, if any needed) so not a particularly super-expensive grade separation compared to quite a few in the Georgetown corridor, and Lakeshore East is going to be much more heavily used when the Whitby maintenance center opens.
-- GTA traffic is predicted to increase over the next 10 years, and electrified trains may run faster as well. Both inceases level crossing risk. Also, above and beyond this, consider increased level-crossing traffic resulting by nearby Guildwood merely getting 15-min two way service.
Based on precedent of Metrolinx doing grade separations, my view is that I think Metrolinx already intends that GO RER will be become fully grade separated within the electricified area (Aldershot/Oshawa/Bramalea/Mt Joy/Unionville terminuses).