You don't give detail of your carriers but as far as I recall Toronto to Gatwick is served by quasi-charter operators Air Transat and Zoom, and some real charter operations such as Thomas Cook Airlines, while Gatwick to Guernsey is in the hands of UK regional airlines Flybe and Aurigny. As they do not have an interline agreement, and as you are presumably travelling on two tickets, both of these conditions do not allow through baggage checking.
Furthermore Gatwick to Guernsey is a UK domestic route and therefore you will need to clear customs anyway, both for your baggage and yourself, when you arrive in the UK. All the airlines involved operate through the South Terminal at Gatwick, so at least it is all in the same building. You will have to check in again as well at the main terminal desks - in the UK gate check in is not common. The Gatwick customs exit comes out close to the check-in desks, just walk round to the right.
The best choice of service to Guernsey is indeed through Gatwick, there are relatively few services to there from other international transit airports. Flights to/from the Channel Islands are renowned for being delayed/cancelled due to morning fog, year round, so going via the only route to Guernsey with multiple daily departures is a good idea.