After having lost every fortress I've used raiding in to the raid corruption bug (although I managed to pull off quite a few in the longest lasting one before corruption hit), I won't use raiding until it's fixed (and my last fortress was lost to "raid" equipment corruption even before starting to send out a raid. My guess is that it was caused by accepting performance troupe petitions (and getting bugged "friendly" units "returning" and hanging out by the embark edges until killed by invaders or insanity).
What types of missions were you running? What was your procedure? I made up some rules for missions that are probably mostly unnecessary, but so far they've kept me from corruption. I still occasionally hit the bug where a dwarf doesn't come back, though.
Since the root cause of the corruption is unknown, any countermeasures are completely speculative. Given that my last fortress got corrupted without any kind of external mission at all (unless you consider exiling or or two dorfs "missions"), my current guess it that the only safe missions are once where the ones sent out are completely naked, own nothing, and bring nothing back.
The missions I made in the fortresses that were corrupted prior to 0.47.04 were mostly raids for artifacts, raids to whittle down the populations, a number of conquests, and some livestock (beak dogs) raids. My expendable squads were made up of non dwarven performers and an occasional sage who'd petitioned and I'd then trained up for about two years and equipped with decent equipment. After a conquest I generally was able to call back about one squad member (the range was something like 0 - 3), with the rest being lost in to the site (not killed, just not available for recall).
I've never had anyone failing to come back for reasons other than death or conquest (not counting trying to raid with dead civs: raiding is completely broken in that case and nobody ever properly leave the embark world tile in that case).