I'm assuming that with this system they are catching like 95% of all cases, since it sounds like the measure is an extremely effective one. Near as I can tell this crime occurs once in every 20000 border crossings. During those 7 years we effectively paid $850 million per person captured.
Now if all 2000 of those people can be demonstrated as terrorists. Heck if only 50 can be captured it may be justifiable. However I wouldn't be surprised if the overwhelming majority of those 2000 cases are absolute nobodies who want nothing more than to live and work in the US. The remaining legitimate criminals caught probably don't justify the cost of the system.
At the end of the day, if someone really wants to enter the US, they are probably not going to enter through our nation's airports. We have thousands of thousands of miles of unprotected border that someone could get across.