Cuprinol is now water-based, so would be incompatible with oil-based fillers. I've used a DAP wood preservative as filler or canvas pre-treat, but a quick web search suggests that is also no longer available and its replacement is water based as well. One thing to watch for with any sort of preservative is the presence of water repellents. Many of these additives are incompatible with subsequent finishes. If the product claims to be paintable, then you may be able to use it to pre-treat the canvas before filling, but I think I'd want to test it thoroughly for compatibility before committing to doing it on a canoe.
Instead of these, I've gone to adding a mildicide paste to my filler - it comes in little packets from the hardware store, and is compatible with oil-based or water-based paints.
Dan