Yes. We discussed this in a number of papers. There are two safer daily alternative drugs in most areas of the world where there's chloroquine resistance, and one is Malarone, which is extremely well tolerated, and true contraindications or intolerance to Malarone are exceedingly rare, with maybe 1%. For the 1% who can't tolerate Malarone, there's doxycycline. The use of doxycycline is maybe discontinued by 20% or more. Far fewer than 1% of people would need to take mefloquine through strict adherence to a policy of use as a drug of last resort.
I don't think it's plausible to imagine a scenario where large groups of soldiers would not be able to deploy were such a policy enacted, and the potential benefits of doing so could be profound.