What is the plural of virus?
Viruses. It is not viri, or (worse) virii. True, the word comes directly from Latin, but not all Latin words ending in -us have -i as their plural.
http://linuxmafia.com/~rick/faq/plural-of-virus.html
The plural of virus is neither viri nor virii, nor even vira nor virora. It is quite simply viruses, irrespective of context.
Suffice to say that I don't find "it doesn't fit comfortably in the mouth of an English speaker" to be a good basis on which to form conclusions about how Latin speakers would decline their vocabulary.
I mean, despite being Greek, I don't particularly object to the fact that most of the Greek loanwords in English fail to fully follow Greek grammar when people speak English. For example, phobias rather than phoboi or phobioi has become the accepted plural of phobia. Heck, people don't even decline my name properly when speaking to me, since English doesn't use the vocative case.