Do you really want to download the entire block chain over Tor? It's possible, but it will take days before you have a functional wallet. You might want to try Electrum. There's a thread here about running it in Tails. A lot of that information should apply to running it in Whonix. In any case, if you still want to use bitcoin-qt in Whonix, what is the problem? Download the tar.gz file from the web site, extract it, and run the 32 bit binary that it contains.