Yes this CA getting into the fretslot on a bound fretboard can be a real pain in the arse and I've spent my time digging it out. I feel your pain! My solution was to not let it happen in the first place. I do this by very lightly tacking the binding in a couple places with the fretboard slot side up and then turn over to the back side to do the real gluing. Also it really doesn't take much CA glue and it is always tempting to over apply. Have not had this problem since.
Actually I take a propane torch to one of those curved StewMac fret slot cleaning blades. Works a charm. If you are doing inlays in a fret board, a trick I learned from Grit Larkin is to fill the slots with plasticine clay before inlaying and then digging it out. The best advice though is just to be real careful and and avoid the situation from the beginning.
I so my fret boards at the front of my CNC so its easy to get to and I cut the purfling slot and inlay the purfling before I cut the fret slots. Never get CA in the slots that way.