I think I have an idea, but it depends on several factors:
1. Do the infected fight each other while untransformed?
2. Do they listen to squad commands?
3. Can you order them to build things?
You might be able to stuff all the infected down a pit to keep them isolated.
EDIT: I opened up my save in Legends Viewer. Apparently there's a weremoose plague in this world. At the end of my turn there were 94 weremoose in existence. Every single one of them is "descended" from a single human who profaned the temple of Mete, goddess of consolation and twilight.
Round 1, Uhol vs Us the uncursed = Lots of dead in the 7/7 water.
Round 2, Metal Kumil rises from the dead as were-moose because the moon is still full. However, the other dead before and after Kumil did not res.
Kumil attack some dwarfs, but kumil suck in military skill. Recruit Onul stayed in he water fighting and dodging. The 3 squads were able to station away from the pool.
Round 3, Kumil reverts back to dwarf. Everything looks ok, but Kumil seems to be upset, interrupting recover wounded, and even dwarfs who wants to give her water. A civilian brawls with Kumil, another civilian joined, and the 4th civilian Stone Astesh had a enough and kills Kumil.
End of rounds, everyone was peace and doing labors. However, unknown to me was the death and Leader Dobar removed all the noble positions. No manager to make the rock hatch orders.
Next Battle, another full moon.
Round 1, 8 dwarfs turns were-moose. We were unprepared. 6 were on the surface, 1 in the farm area, 1 midway to forge in central stairs.
Possible burrow would be the north ramp, but it's a one way in and one way out.
Next burrow is no-door, no-hatch rooms connected to central pit, with stairs from noble rooms, down to the targetted arena level, around 4z in total. This has a dig hallway to central stairs. I made the burrow here, and 14 made it ok, until once of the were started moving towards it. Miner Logem lead it away to the surface without micro-managing.
Round 2, currently. No more berzerk were-moose. However, only 10 or 11 are citizens or controllable.
The others are listed as Units, but cannot be given labors, nor be set to military.
And in this round 2, some dwarfs are still brawling.
All I know so far is Miner Goden is continuing to mine the rooms below the current bedrooms. Each is a ramp + 1 tile for door + a 3x3 room.
If I cannot set these infected into the military, the untainted 10 (or 11) dwarfs will be in 2 squads and find a seal-able room until some control is established.
1. Open the caverns, maybe the infected will go out there and occupy themselves.
2. Create a tavern, library, and temple for all visitors and let them deal with each other.
3. Wait patiently for control, keep working on arena, then have a nice gem windows to view the fights.
I might as well spoil my plans, as I it will be difficult.
I envision an circular arena, at least 20 wide in diameter.
Fit a 1x2 bridge as entrance to the arena + 1 tile statue + 1 tile room, + 1 tile up ramp locked with a hatch above.
The idea is to assign the statue + 1 tile room + ramp into a temple, and lock choice visitors there.
If they go insane, tantrum, or berzerks, they might topple the statue creating some curses.
Upon the curse, 1x2 bridge can be-opened to the arena.
the 1st floor z+0 is the the arena floor, either featherwood logs for their whiteness, or just use quartzite since we have plenty.
the 2nd floor z+1 of the arena floor will be natural stone, smoothed and unclimb-able.
the 3rd floor z+2 will be fortifications for marskdwarfs
the 4th floor z+3 will be noble rooms with gem windows, and maybe some common rooms too.
the 5th floor z+4 would be dirt/clay loam.
the 6th floor z+5 would be the surface, with a building that can be used to pit caged visitors.