"What is the relative effectiveness of AI safety research vs. bio risk research?"
If you had a precise definition of "effectiveness" this shouldn't be a problem. E.g. if you had predictions for "will humans go extinct in the next 100 years?" and "will we go extinct in the next 100 years, if we invest 1M into AI risk research?" and "will we go extinct, if we invest 1M in bio risk research?", then you should be able to make decisions with that. And these questions should work fine in existing forecasting platforms. Their long term and conditional nature are problems, of course, but I don't think that can be helped.
"How much value has this organization created?"
That's not a forecast. But if you asked "How much value will this organization create next year?" along with a clear measure of "value", then again, I don't see much of a problem. And, although clearly defining value can be tedious (and prone to errors), I don't think that problem can be avoided. Different people value different things, that can't be helped.
One solution attempt would be to have an "expert panel" assess these questions
Why would you do that? What's wrong with the usual prediction markets? Of course, they're expensive (require many participants), but I don't think a group of experts can be made to work well without a market-like mechanism. Is your project about making such markets more efficient?