I think your fix ideas are great. Call it overkill if you want but I will be installing a bilge pump on my kayak to avoid exactly what you are talking about. Having that is worth the extra battery weight.
Also check out Youtube, I recall seeing a video about the Stealth Bait tank installation that CJ did and he talks about the over flow holes.
http://www.youtube.com/watch?v=snGUpj2MAao