There are some epoxy fillers that have certain paint adhesion problems, but I haven't had any with graphite powder as long as it's cleaned of any blush and properly sanded first. If I didn't have any colloidal silica on hand, I'd just use a graphite/epoxy mixture. It will be a bit softer than the same with a bit of colloidal silica added to harden it, but it''s still pretty tough stuff. The sand may also be made of silica, but it's in a very different form and I don't think it will do the same job. I'd be worried that I might be creating a finish that sticks on river rocks and ledges like crazy - when I'm actually trying to coat the boat with something slippery. It might also be a real bear to sand smooth and get ready for paint.
Dan, you are correct. If painted over, the graphite will do nothing until a rock scrapes through the paint, exposing it. At that point it can, in some cases, help the canoe slide off a rock. Whether or not it slides off with less damage than plain varnished epoxy filler coats would have sustained is a whole different debate. Most people do leave the graphite surface unfinished (either just as rolled on, or sanded smooth) to cut down on paint repairs. It tends to look a little lumpy if you don't finish sand it, but once sanded it has a pretty nice charcoal satin look to it and is pretty easy to patch when needed. It's kind of a messy sanding job because of the black dust. The graphite content blocks UV at the surface, so a varnish topcoat isn't needed as a UV shield.