Youre probably perfectly fine. It certainly has completely dried out by now, and bad bugs need moisture in which to survive.
The Sweetwater maintenance kit
But sure, you want to be safe. Id simply run water through itclean, fresh water. Pump it for five minutes or so. If youre feeling unlucky, first make up a 10-to-1 mix of water and bleach, pump that through for a few seconds, let it sit for a minute, then pump it through with regular tap water. You also can take the filter core out and clean it with a brush.
Do check the O-rings on the filter. While yours is not that old, O-rings get dry and will crack. So make sure theyre all look good. Maybe even replace them, just for luck. MSRs maintenance kit for the Sweetwater ($20) has all the stuff you need, although you can buy the right O-rings and silicone grease at your local home improvement store for $5.
So, no worries. A few precautionary steps, perhaps a little preventative maintenance, and your Sweetwater is fine. Drink up!