Do bike thieves really go to the bother to drag their stolen goods over to the local bike co-op as a donation?
We only run the serial numbers of obviously high-value bikes (which is just a quick serial number search on CPIC, the Canadian police database); we don't record the numbers unless we have strong reason to believe it prudent. (Because, frankly, most bike owners don't record them either.) CPIC has a terrible web interface, so we made our own to make the process less cumbersome.
I can't imagine this being worth the effort it would require of your organization. If your police are insistent, perhaps you could request a pilot: do it for 3 or 6 months, and re-evaluate: if some arbitrary percentage of success rate isn't achieved (e.g. if less than 1% of bike donations are actually related to theft), then you have pretty strong evidence that it's a waste of time. It'd probably be more efficient to just set up camp at the local university and catch bike thieves in the act. (Which itself is probably not very efficient, but at least it'd generate some fantastic media coverage if you succeeded.)
On the other hand, if the evidence actually shows that you are helping to recover stolen bikes, then you can decide at that time if you want to develop a system other than a basic spreadsheet.