If several engineers repair the same buildings, that's called a good defense (of that one building). Keep in mind that these engineers are not available for other tasks or for attacking the enemy. So if that one building is decently defended, the attackers has to do a little bit of teamwork himself and go for another one; the defender can't have multiple engineers in every building.
As for the repair cost in $$$: I would think that this is a very bad idea. Engineers already have a tought job that not many people really like to do, mostly keeping inside the base seeing little actuion, being armed with sub-par weapons, but nevertheless a job that is critical to success; they are the enablers and force multipliers. Without engineers, no vehicles get repaired, no buildings get repaired, no beacons get disarmed, and no on lay minefields or even watches our for infiltrators. So if doing that kind of job also means having to LOSE money for essentially doing what your class is meant to do, who would still choose an engineer over a more combat-oriented class? There has to be some kind of reward or no one would do this job.
TL;DR: If a maaster terminal is spam-repaired by engineers, choose a different building to attack. Brute force with five Mammoth Tanks can work sometimes, but most victories get scored by a small band of infiltrators who manage to c4 and nuke critical enemy structures.