That suggests that the system is near perfect as is. If people know Linux is faster but that they will not get any more points for using Linux most will not bother trying to use Linux. It'€™s the badge system than encourages people to crunch more slowly not the points system. The points system is just an obstacle that is preventing advancement. Many crunchers have crunching rigs that they just use for crunching. Appropriate more points for faster crunching and they will use Linux and expedite the research. So fixing the system will speed up the research, not slow it down.
While the credit system in use is structured by Boinc, it does not necessarily need to be adhered to in its broken form. It is down to the WCG to use a more correct points system. Doing so would encourage people to use Linux and thus do more work. The exact adaptation of the Boinc system is down to the WCG. Other projects deal with this better than the WCG is presently doing and benefit accordingly.