Before you do, try it on scrap canvas, let it dry completely and then test with some filler. The Scotchguard is most likely a fluorocarbon repellant, rather than a silicone compound but even so, one of its typical main functions is to prevent stuff from sticking well to cloth fibers. In fact, I'd do two tests, maybe 12" square, one sprayed, one plain. Then fill both, let it harden properly and then flex them a bit to see if there is and difference in the bond strength. The idea of what a mess you would have on your hands if the filler started peeling off of a new canoe should be enough motivation to conduct some tests.