Of course, that's perfectly fine. It's really about time that Google killed off the app, which had been born as a Google Labs project back in 2009. The app was always extremely barebones, and one of the best things about it was that it was free, which isn't really much of a separator in the Play Store. So, Google is pulling the plug, because there are plenty of alternatives in the Play Store.
According to the release, the app will continue to function if you have it installed, but it has been removed from the Play Store, and as of November 1st, the search function will stop working. But, the good news is that because Listen always used Google Reader to save your podcast subscriptions, those will stick around, and you can save them whenever you'd like.