The best way to fight Geists is to not fight them at all; Workers will never bother the player and will usually stay clear of firefights. Destroying them to kill enemies is often a good idea, but it is necessary to be cautious since their explosion can easily chain-react and kill a large group of Geists; it does not appear to deal any damage to BJ, only to enemies. Geists are also vulnerable to fire from enemies and explosions while BJ is in the Veil, and jumping on a Geist will kill it instantly.
While fighting the Queen, BJ is in a Flakvierling 38 he cannot leave, and so must kill the Warrior Geists and suicide Geists using this. Warrior Geists will generally run to the sides of the emplacement to attack, while the suicide Geists will appear and then move straight towards it.