Very true.
Even the best "lie detector" could only prove what someone believed or remembered to have happened. Many studies have shown memories to be very open to manipulation, children have been convinced by their doctors that they were raped by their own parents (when they were not). People have been manipulated to believe that certain individuals (who look nothing like the real perpetrators) committed acts of violence against them.
Even without overt manipulation, eyewitness testimony is notoriously unreliable, and there is no reason to believe that even suspects who have not been coerced might come to believe falshoods about their own actions through some combination of internal and external pressure.
Furthermore, as one with personal experience with fMRI data analysis, the though of using fMRI to sentence someone to years in prison or worse is frightening. While over large sample groups certain types of analysis can be reliable, fMRI data is frought with noise, is very low resolution (both spatially and temporally), and due to the huge amount of pre-processing required to get any useful data, would be very vulnerable to manipulation by unscrupulous types (or merely accidental bad analysis by poor technicians or bad software).