The fact that you can mod means that you can make new units and dump them on the internet. This will mean that less and less people will buy their trashy, overpriced DLC. That means less profits. CA isn't a charity, but a commercial company, this means they will maximize profits. And if mods prevent them from gaining some extra bucks they will eliminate EVERY possiblity to make mods.
I've said this before...if I was smart enough to advise CA on the best avenue to take, I'd be making money with my own company. That said, I hold up Bioware as an example of how to do things, IMHO. I haven't played DA, so I don't know the latest Bioware policies, but Baldurs Gate & NWN had a thriving mod community, and actually increased interest and sales form what I've seen. I just know that I was more willing to buy Bioware products, first because they put out great games, and second, because I knew I'd be playing the mods for a long, long time.