If someone came up with a reliable and fair system to payout gridcoin for BOINC work independent of the projects you choose, that would be great. But I doubt that this is possible with the current BOINC reward system.

Actually, I don't think the current reward system is bad. Who are we to decide which scientific research is more important and by which percentage. What if seti@home really discovers something? Then everyone who said this is nonsense would be proven wrong. I beliefe BOINC is attractive for projects with low funding and enables scientists to research in fields with low interest by large investors. It would be way easier to run your calculations on a huge compute cluster if you had the money.
So if we made the distribution of rewards scewed towards WCG for example and everyone thinks that curing cancer is more important than everything else, the other projects would not get their computations done. In the case of WCG you could also argue that they have an advantage over smaller projects because they are supported by a huge company (IBM).
But you can still make your own choices. Take Hive account@dutch as an example. He has figured out that he has other motivations than money to choose a project. (ethics, advertising his research lab, the pride beeing in a specific journal)
As I see it, if you move away from the projects you like for the money, it is your decision and you have to live with it. There will be people like Hive account@dutch that come to the conclusion that money is not everything and support what they think matters. But people have different opinions and preferences, we should not determine which project is important and which is not. We don't know that and we cannot be objective about that.
And the people that are switching projects for the money also help smaller and less popular projects to get their research done. And that is also very important.