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Good Wood Filler for De-Fret

Veneer. All the way. It's really easy and you can vary the color. I might be the worst woodworker on Earth and it was no problem (I did have an expert guide me through it).
Probably gonna want to shim the neck, though (did that with veneer also). But you probably already know that. I didn't.
 
Wood filler is cosmetic by design. It is to be looked at, not relied upon to stiffen a kerfed board.

The fingerboard needs a structural fill, something that will not compress under tension. Or at least won't compress very much. Wood veneer, especially of the same species or a species that is as hard, is the best. Plastic binding material is also used to great success.
 
Standard wood filler is not a great idea, but there are other fillers to consider if you don't want veneer. If you don't want the lines to show as much you can use a pu or epoxy based hard and clear finish and mix it with sanding dust from the fingerboard. Imo this is not very pretty if the grain in the wood is very visible, but I've had good results with ebony. With something like rosewood I'd go the veneer way. Also some woodtypes can chip very easily along the edges of the slot. Filling it this way can fix that. When the slots are chipped from removing the frets you can also combine this method with veneer to fill in and camouflage the chips.