What happens to scientific theories when definitions change or new information comes to light? A question in the Co-op

I love this exchange, and I thought many of you would too. There has been quite a bit of interest about homeschooling science co-ops based on the number of hits the co-op blog posts on this site are getting. This is an email I received recently from someone who is teaching one. I have also included my reply. 
Email to me Tue, 16 Sep 2014 20:41:45 -0400
I just started teaching biology for my co-op out of your book (thanks for the notes on your blog on teaching it in a co-op btw), and I’ve had the kids watch the full program of BBC hidden universe, secret life of a cell https://www.youtube.com/watch?v=FFrKN7hJm64 which pretty much convinced the kids that viruses were alive, which meant that during the debate on whether viruses were alive or not, they decided that the definition of living was outdated and needed to be changed.
The very big problem was chapter 2 – this week, right after I explained the difference between a scientific theory and non-scientific theories, we came to cell theory, and one of the students pointed out that if viruses are alive, cell “theory” isn’t true. Please help, I’m sure there is a good explanation I can give the kids, I just don’t know it. I’ve looked through a bunch of internet articles, and the consensus seems to be that a virus is definitely not a cell, and there may be a new classification of alive.