What about Viruses?

I recently attended a lecture on viruses and it never ceases to amaze me how successful these little snippets of genetic material have become at self-replication. In fact, making copies is basically all they do. Viruses exist solely to reproduce. They are little more than a protein coat holding rouge bits of DNA or RNA with just enough instructions to hijack a cell and cause to be make more protein coats and copies of the code. As things that aren't generally considered to be alive, these pesky little guys are amazing case studies for evolution and natural selection.
I bring this up because proponents of Intelligent Design originally tried to make the case that ID should be considered a "Science" on equal footing with evolution. It was not a "religion," they claimed, because the "Designer" could be any intelligent being/deity/cosmic force. Of course, the Cristian God was identified as the "Designer" much more often than Zeus or an anomalous probability wave. The Dover decision made clear that this was nothing more than a sham, and the recent movie Expelled doesn't even try to mask the connection. But even before the pro-ID bunch abandoned all semblance of "non-denominational" Intelligent Design, there was, and is, a huge logical problem. If a "Designer" is necessary for life to have come into being, how could viruses exist unless he/she/they/it also made them? And for that matter, what about genetic diseases or birth defects? A "Designer" intelligent and powerful enough to make all life could certainly have done a better job or at least left our the worst disease causing germs. There is a need for something of a "theology" about why things sometimes don't work, be it Pandora's box or Eve's Fruit or some other creation myth. The only alternatives are to say that either the "Designer" harbors come malicious intent or has some secert plan beyond the ken of mere mortals. Only the latter is acceptable to most adherents, but even this is a "theology" in its own fashio. The truth is there can be no coherent theory of Intelligent Design without making claims regarding the "Designer(s)," which is why it was correct identified as religion, not science.