Re: Decommissioning through hulls?
My wife and I have done a lot of fiberglass hull repairs on our boats. It's not rocket science. There are a lot of good books on the subject that can take you through the process step by step, follow them closely, but don't be anal about it. Don't be impatient (let the layers cure). Don't skimp (especially on the hole size preparation). And above all recognize that you can rectify a mistake.
Having said all that, I'd say your in good shape leaving the seacocks in place, giving them a good greasing before closing and plugging them. It wouldn't hurt to even exercise them on occasion.
The only reason I'd leave them in is potential resale. No matter how good some people feel about composting toilets, others don't have the same warm and fuzzy felling about them. If you're looking to sell the boat later on the ability to convert back, if the new owner so chooses, is a selling point.