I've always and only managed bitcoin-qt manually in my instances. Have you considered just removing the functionality for managing Bitcoin Core automatically, and just replacing it with a "Tell me how to connect to your bitcoind [Default 127.0.0.1:8333]" and "Where do the blocks live [Default %USERDATA%\bitcoin or whatever]" in Options?

Add a note to the documentation that Armory requires a locally running bitcoind, and will need to be told how to connect and where the blocks live?  At least then people having trouble with bitcoind wont be bugging you....