Sorry to bump
But balancing keeping the use of alien weapons outside of a single skirmish is not insurmountable at all.
1. Make the alien ammo degrade pretty fast you for example you could make total alien ammo half itself each day as its base rate or even faster
2. Add repeatable research to slow the degradation as a moderate research sink. This would give a "cost" to using alien weapons over researching better home grown alternatives
3. Give the aliens a tier of weapons which I think would make the game more interesting overall
Each tier would have its own "ammo" to slow the degradation each type would have to be researched separate so for example after a significant amount of time you could get tier 1 degradation to almost nothing but then at tier 2 ammo degrades really fast again unless you pour MORE significant time into researching it.
example alien tiers
Tier 1 Gamma ray lasers
Tier 2 Plasma
Tier 3 Molecular disintegrators
and obviously you would keep the alien weapons accuracy penalty
Doing all of this gives an interesting stop gap alternative to researching actual weapons while allowing you to use those cool alien weapons at least for a little bit.