Certainly anti-malarials have been provided for a fairly significant period of time, certainly predating mefloquine. We can't really speak to given missions at this point, but we do know that doxycycline had been used, and chloroquine was used in certain areas where the malaria is not resistant to chloroquine.
All of these medications have side effects. Some of the studies even suggest in terms of the side effect profile that although the particular symptoms are different, the actual numbers of side effects are similar between mefloquine and doxycycline, for example. In fact, the discontinuation rate of the two medications is about the same.