There is essentially very little chance of succeeding in the MAGMA mission line without an osprey or similar craft (the first mission in MAGMA lab with all the zombies will overpower you - the mission can be a close call even with in higher difficulties with a bad spawn). So for all practical purposes, chasing down this line will have to wait until you've deal with at least some of the cults. By then you should have Promo III, and you will be in mid-late 1998. You could even already have Kitsune by then.
Pulse weapons, especially when combined with chem clips, can be extremely deadly, especially against less armored foes, like zombies. Much better than puny rifles. (I never even bother with them.) But if you'd just have to pick one gun in before and about Promo-III era (and you don't), I'd probably still pick a BO auto-sniper, because it will be very workable against any enemy unit. The second contender for one of the best weapons would be TAC grenade launcher with gas grenades.