Working now. yum has found bitcoin.x86_64 0:0.9.2.1-1.fc20 again, and the Qt wallet is working as it was. Thanks error!
The situation with using bitcoind/bitcoin-server as a service is still difficult with Qubes. I believe what's happening is mirroring what happens also with bitcoin-qt when it's configured to use /var/lib/bitcoin as the datadir, namely that the blocks download but aren't/cannot be written to disk (if I quit and restart bitcoin-qt when it's reportedly dl-ing the blockchain to /var/lib/bitcoin, the block count starts from 0). If I run systemctl start bitcoin, Armory detects that bitcoind is running, but it doesn't see any new blocks, so it appears that bitcoind is behaving the same way bitcoin-qt does, despite having permission to access /var/lib/bitcoin. I'm thinking that this is because Qubes has SELinux set disabled by default (yum install bitcoin-server yields a page of permissions warnings).
It'd be incredibly cool to get bitcoind/bitcoin-server working as a service on Qubes-OS, using Armory would appear much less cluttered. However, I've figured out how to establish a Bitcoin-Qt desktop item that runs in Node mode (-disablewallet argument), so it's not so bad this way. Does Qubes need it's own dedicated package to install and configure bitcoind? I'm thinking that's possibly the case.
I'm not sure what the deal with Qubes OS is. When I get some time I'll play with it and see if I can figure out what's going on. I can't make any guarantees, though; it seems they have a completely different security model and who knows what it will need to run the bitcoin server successfully.
Right now, though, the more important thing is doing something about this horrible configuration file handling code. It's old, old code from Bitcoin that isn't at all object oriented and is very brittle. It got even more brittle with the 0.9 refactoring, which is where this latest issue came from. I _finally_ think I have a workaround, but I'm going to give it a few rounds of testing locally before I push it out. Eventually all this code really needs to be scrapped and rewritten.