There are exceptions to avoiding missiles on extraction. Reactor and Ghost are good examples of a map where it's best to stay far away from the extraction point as long as possible. Draw all the enemies away. With 20 secs to go, run to extract. You may need missiles to get there. But there are always one or two who camp the extraction point, so when smarter players run there with a few seconds to go, there will be bosses everywhere. Missiles will be needed to stay alive. And the campers will be dead.
Rio is an example of the opposite. If even one player gets to the extraction point before the spawn starts, all the enemies will spawn at the other end. One or two competent players can camp the extraction end and keep the enemies out. If you can't get to the extraction end before the spawn starts there, clean it out with missiles, and then hold it. This only works on Rio, as far as I know, but it works well there.
For some unknown reason, everyone camps the extraction point in Hydra. Don't know why. The best strategy then is for one strong player to hold the back corridor, which can be done without missiles, while the other three hold the extraction point. As long as the back corridor is held to the end and missiles are avoided as long as possible, it usually goes smoothly. But if the back corridor is abandoned for even a few seconds, enemies will spawn there and overrun the team.
Generally, then, missiles should be used if necessary at the last seconds at the extraction spot, but delayed as long as possible so as not to swamp the team with bosses with too much time left. They should be avoided elsewhere because they screw up the spawns.